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https://github.com/cmdcolin/awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
https://github.com/cmdcolin/awesome-genome-visualization
List: awesome-genome-visualization
genome-browsers genomic-visualizations
Last synced: 2 days ago
JSON representation
A list of interesting genome browser or genome-browser-like implementations
- Host: GitHub
- URL: https://github.com/cmdcolin/awesome-genome-visualization
- Owner: cmdcolin
- Created: 2019-12-17T07:23:06.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2024-04-12T22:04:05.000Z (10 months ago)
- Last Synced: 2024-04-14T12:32:06.715Z (10 months ago)
- Topics: genome-browsers, genomic-visualizations
- Language: TypeScript
- Homepage: https://cmdcolin.github.io/awesome-genome-visualization/
- Size: 60 MB
- Stars: 715
- Watchers: 24
- Forks: 96
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
Awesome Lists containing this project
- awesome-awesomeness-bioinformatics - Awesome Genome Visualization - browser-like implementations. (Awesome)
- ultimate-awesome - awesome-genome-visualization - A list of interesting genome browser or genome-browser-like implementations. (Other Lists / Julia Lists)
README
# awesome-genome-visualization
A list of interesting genome visualizers, genome browsers, or
genome-browser-like implementations
See the new companion website here
https://cmdcolin.github.io/awesome-genome-visualization/
Follow the BlueSky https://bsky.app/profile/awesomegenomeviz.bsky.social or Mastodon account https://genomic.social/@awesomegenomevisualization
Note that the organization on the GitHub README here is a best effort
categorization using the first tag applied to each tool, but tools can have
multiple tags too. See the website to see all tags applied to tools
The general focus here is on tools that plot things in genomic or sequence
coordinate space
Note: This list runs the gammut from bespoke and simple to more general-purpose
and complex tools. Some are historical, or may be for more visual inspiration
only
I also encourage you to make your own visualization, things like R make this so
much easier! But also consider making your visualization code re-usable for the
wider community! And feel free to send PRs for more tools!
## Academic license
- [Consed](http://bozeman.mbt.washington.edu/consed/consed.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/consed.png)
## General
- [ABrowse (genome browser)](undefined) (Had integrations with BioMart, Taverna)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/abrowse2.png)
- [Argo](https://web.archive.org/web/20070924141423/http://www.broad.mit.edu/annotation/argo/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/argo.png)
- [BasePlayer](https://baseplayer.fi/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/baseplayer.png)
- [Biodalliance](http://www.biodalliance.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/biodalliance.png)
- [Celera genome browser](https://www.csee.umbc.edu/~turner/presentations/bvw2002/sld009.htm)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/celera.jpeg)
- [Ensembl genome browser](https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ensembl.png)
- [Ensembl genome browser 2020 edition](http://2020.ensembl.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/2020ensembl.png)
- [GBrowse 2](http://gmod.org/wiki/GBrowse) (Original gbrowse paper
https://doi.org/10.1101/gr.403602)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gbrowse.png)
- [GenomeMaps](http://www.genomemaps.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomemaps.jpg)
- [Genoverse](https://github.com/wtsi-web/Genoverse)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genoverse.png)
- [Gosling](https://gosling.js.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gosling.png)
- [gtracks](https://gitlab.com/salk-tm/gtracks) (Powered by pyGenomeTracks)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtracks.png)
- [HiGlass](https://higlass.io)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/higlass.png)
- [IGB](https://bioviz.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/igb.jpg)
- [IGV](https://igv.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/igv.jpg)
- [IGV.js](https://github.com/igvteam/igv.js/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/igvjs.png)
- [JBrowse](http://jbrowse.org/jbrowse1.html) (See also JBrowse plugin registry
https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app
using Electron)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbrowse.png)
- [JBrowse 2](http://jbrowse.org/jb2) (See gallery for more examples
https://jbrowse.org/jb2/gallery)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbrowse2.png)
- [Kero-BROWSE](https://kero.hgc.jp/examples/CLCL/hg38/index.html) (Also can
visualize basic synteny, see tracks e.g.
https://kero.hgc.jp/tool/keyword.html#kero:chrX:153,724,868-153,744,762 human
vs chimp)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/kerobrowse.png)
- [NCBI Genome Data Viewer](https://www.ncbi.nlm.nih.gov/genome/gdv/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gdv.png)
- [Nucleome browser](https://vis.nucleome.org/v1/main.html) (github at
https://github.com/nucleome)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/nucleome.png)
- [Pileup.js](https://github.com/hammerlab/pileup.js)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pileupjs.png)
- [Savant](http://bioinformatics-ca.github.io/savant_genome_browser_lab_2015/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/savant.jpg)
- [Tablet](https://ics.hutton.ac.uk/tablet/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tablet.jpeg)
- [trackplot (python)](https://github.com/ygidtu/trackplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackplot_python.png)
- [Trackster](https://galaxyproject.org/learn/visualization/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackster.png)
- [UCSC genome browser](https://genome.ucsc.edu/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ucsc.jpg)
- [UTGB (University of Tokyo Genome Browser)](http://utgenome.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/utgb.png)
- [Valis browser](https://valis.bio/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/valis.png)
- [WashU epigenomics browser](https://epigenomegateway.wustl.edu/) (The ReactJS
is a redesign, there is also a legacy version. Note also, there are
comparative features
https://www.biorxiv.org/content/10.1101/2022.11.29.518374v1)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/washu.png)
- [Zenbu](http://fantom.gsc.riken.jp/zenbu/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/zenbu.png)
## Alignments viewer
- [alignoth](http://htmlpreview.github.io/?https://github.com/koesterlab/alignoth/blob/main/examples/plot.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignoth.png)
- [bamscope](https://github.com/jslfree080/bamscope)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamscope.png)
- [Chromatic](https://chromatic.nci.nih.gov/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromatic.png)
- [DrukBam](https://github.com/StephanHolgerD/DrukBam)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/drukbam.png)
- [Gambit](http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gambit.png)
- [GenomeView (java app)](https://genomeview.org/content/quick-start-guide)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeview_java.png)
- [gw](https://github.com/kcleal/gw)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gw.png)
- [Hawkeye](https://github.com/peterhj/amos)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/hawkeye.png)
- [LookSeq](https://www.sanger.ac.uk/tool/lookseq/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/lookseq.png)
- [MagicViewer](http://bioinformatics.zj.cn/magicviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/magicviewer.jpeg)
- [MapView](https://sites.google.com/site/wjwdavy/) (links in original paper are
dead, but URL provided here works)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mapview.jpg)
- [NGB](https://github.com/epam/NGB)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ngb.png)
- [pyBamView](https://mgymrek.github.io/pybamview/) (See supplementary info for
more figures, supports padded SAM/BAM which is fairly rare)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pybamview.png)
- [Staden](https://sourceforge.net/projects/staden/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/staden.png)
- [udon](https://github.com/ocxtal/udon) (Uses an advanced data structure for
pileup, so visually a basic example but likely just a small demo)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/udon.png)
- [wally](https://github.com/tobiasrausch/wally)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wally.png)
## Annotation
- [Varsome]()
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/varsome.png)
## Assembly
- [GCI](https://github.com/yeeus/GCI)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gci.jpg)
## Assembly QC
- [ALVIS (chimeric alignment viewer)](https://github.com/SR-Martin/alvis)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alvis_chimeric.png)
- [Icarus QUAST](http://quast.sourceforge.net/icarus.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/icarus.png)
- [MIRA](http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html)
(orig paper also describes mira here
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mira.png)
- [vega](http://vega.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=6-QBL)
(Mentioned in
https://www.biorxiv.org/content/10.1101/2021.07.02.450883v1.full.pdf also
note: vega standards for vertebrate genome annotation database)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vega.png)
## BLAST
- [SequenceServer](https://sequenceserver.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequenceserver.png)
## Chromosome painting
- [GeMo](https://github.com/SouthGreenPlatform/GeMo)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gemo.png)
## Circular
- [Anvio](https://peerj.com/articles/1319/)
- [BioCircos.js](http://bioinfo.ibp.ac.cn/biocircos/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/biocircos.png)
- [BRICK (BRIG-like circular knowledgebase)](https://brick.ink/) (See also BRIG)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/brick.png)
- [CGView](http://cgview.ca/) (See also CGView comparison tool and other related
https://paulstothard.github.io/cgview_comparison_tool/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgview.png)
- [Circleator](http://jonathancrabtree.github.io/Circleator/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/circleator.png)
- [circlize](https://github.com/jokergoo/circlize)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/circlize.jpeg)
- [Circos](http://circos.ca/) (no official github to my knowledge)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/circos.png)
- [CircosJS](https://github.com/nicgirault/circosJS)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/circosjs.png)
- [circularMT](https://github.com/msjimc/circularMT)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/circularmt.png)
- [DNAPlotter](https://www.sanger.ac.uk/science/tools/dnaplotter)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaplotter.jpg)
- [GenomeProjector](https://github.com/gaou/g-language/wiki)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/glanguage.jpg)
- [genoVi](https://github.com/robotoD/GenoVi)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genovi.png)
- [Gview](https://server.gview.ca/examples)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gview.png)
- [JupiterPlot](https://github.com/JustinChu/JupiterPlot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jupiterplot.png)
- [OGDRAW](https://chlorobox.mpimp-golm.mpg.de/OGDraw.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ogdraw.png)
- [OmicCircos](http://bioconductor.org/packages/release/bioc/html/OmicCircos.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/omiccircos.png)
- [pyCirclize](https://github.com/moshi4/pyCirclize)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pycirclize.png)
- [pyCircos](https://github.com/ponnhide/pyCircos) (See also
https://github.com/ponnhide/plasmidviewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pycircos.png)
- [RegulomeExplorer](http://explorer.cancerregulome.org/all_pairs/?dataset=TCGA_ACC)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cancerregulome.png)
## CNV
- [aCNVViewer](https://github.com/FJD-CEPH/aCNViewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/acnvviewer.png)
- [BAMScale](https://github.com/ncbi/BAMscale)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamscale.png)
- [bcftools cnv](https://samtools.github.io/bcftools/howtos/cnv-calling.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bcftools_cnv.png)
- [CNANorm](https://www.bioconductor.org/packages/release/bioc/html/CNAnorm.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnanorm.png)
- [CNSpector](https://github.com/PapenfussLab/CNspector)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnspector.png)
- [cnvCurator](http://www.acsu.buffalo.edu/~lm69/cnvCurator)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvcurator.png)
- [CNVkit](https://cnvkit.readthedocs.io/en/stable/plots.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvkit.png)
- [copynumber](https://www.bioconductor.org/packages/release/bioc/vignettes/copynumber/inst/doc/copynumber.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/copynumber.png)
- [CoveragePlotter](http://lindenb.github.io/jvarkit/CoveragePlotter.html) (See
also http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html for
multi-chromosome)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/coverageplotter.png)
- [covviz](https://brwnj.github.io/covviz/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/covviz.png)
- [genevisR](https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genevisr.png)
- [genome_coverage_plotter](https://github.com/matted/genome_coverage_plotter)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome-coverage-plotter.png)
- [GenomePaint](https://genomepaint.stjude.cloud/) (Demos
https://proteinpaint.stjude.org/bam/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomepaint.png)
- [GenomeSpy](https://genomespy.app/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomespy.png)
- [Genovar](http://genovar.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genovar.png)
- [mocha](https://github.com/freeseek/mocha) (Has a full analysis pipeline
associated with end result visualizations)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mocha.png)
- [Orchestral](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/orchestral.png)
- [PURPLE](https://github.com/hartwigmedical/hmftools/blob/master/purity-ploidy-estimator/README.md)
(intermutation-distance rainfall plots/katagesis plots are not technically in
genomic coordinates, but do indicate genomic cluster of variants)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/purple.png)
- [SeeNV](https://github.com/MSBradshaw/SeeNV)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seenv.png)
- [sequenza](https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html#plots-and-results)
(also see https://sequenzatools.bitbucket.io/#/home)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequenza.png)
- [SFARI](https://gene.sfari.org/database/human-gene/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sfari.jpg)
- [SnoopCGH](http://snoopcgh.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/snoopcgh.jpg)
- [SNPitty](https://bitbucket.org/ccbc/snpitty/src/master/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpitty.jpg)
## Commercial
- [10x genomics/Loupe](https://support.10xgenomics.com/genome-exome/software/visualization/latest/structural-variants)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/10xgenomics.png)
- [Alamut](https://www.interactive-biosoftware.com/alamut-visual/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alamut.png)
- [ATCC Genome Portal](https://docs.onecodex.com/en/articles/3996697-using-the-genome-browser)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/atcc.png)
- [Benchling](https://www.benchling.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/benchling.png)
- [Bionano](https://bionanogenomics.com/technology/structural-variation/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bionano.png)
- [Circa](https://omgenomics.com/circa)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/circa.png)
- [CLC Genomics workbench](https://digitalinsights.qiagen.com/news/blog/discovery/structural-variant-detection-using-clc-genomics-workbench/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/clcgenomics.png)
- [DNASTAR](https://www.dnastar.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnastar.png)
- [ERGO](https://www.igenbio.com/ergo)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ergo.png)
- [Geneious](https://www.geneious.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneious.png)
- [Genestack](https://genestack.com/blog/2015/05/28/navigation-in-genestack-genome-browser/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genestack.png)
- [Golden Helix](https://www.goldenhelix.com/products/GenomeBrowse/) (Free for
academic use)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/goldenhelix.png)
- [Lucid viewer](https://lucidalign.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/lucidalign.png)
- [MacVector](https://macvector.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/macvector.png)
- [Persephone](https://persephonesoft.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/persephone.jpg)
- [SnapGene](https://www.snapgene.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/snapgene.png)
- [Strand NGS](https://www.strand-ngs.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/strandngs.png)
## Comparative
- [AccuSyn](https://accusyn.usask.ca/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/accusyn.png)
- [Aequatus](https://github.com/TGAC/Aequatus)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/aequatus.png)
- [AliTV](https://alitvteam.github.io/AliTV/d3/AliTV.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alitv.png)
- [Artemis comparison tool (ACT)](https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/artemis_act.png)
- [asynt](https://github.com/simonhmartin/asynt)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/asynt.png)
- [AutoGraph](http://autograph.genouest.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/autograph.png)
- [BactoGENIE](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bactogenie.png)
- [Biodalliance comparative demo](http://biodalliance.org/dev/test-comparative.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/biodalliance_comparative.png)
- [BRIG](http://brig.sourceforge.net)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/brig.jpg)
- [Chromatiblock](https://github.com/mjsull/chromatiblock)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromatiblock.png)
- [CHROMEISTER](https://github.com/estebanpw/chromeister)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromeister.png)
- [chromoMap](https://lakshay-anand.github.io/chromoMap/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromomap.png)
- [chromsyn](https://github.com/slimsuite/chromsyn)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromsyn.png)
- [Cinteny](http://cinteny.cchmc.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cinteny.png)
- [clinker](https://github.com/gamcil/clinker)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/clinker.png)
- [CMap](http://gmod.org/wiki/CMap)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cmap.jpg)
- [CoGe](https://genomevolution.org/coge/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/coge.png)
- [Combo](undefined) (Based on the tool 'Argo')
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/combo.png)
- [Comparative assembly hub / "snake track"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/comparative_assembly_hub.png)
- [CrossBrowse](https://github.com/shenkers/CrossBrowse)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/crossbrowse.png)
- [CrowsNest](https://pgsb.helmholtz-muenchen.de/crowsnest/help.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/crowsnest.png)
- [CVit](https://sourceforge.net/projects/cvit/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cvit.png)
- [Cvit.js](https://github.com/LegumeFederation/cvitjs)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cvitjs.png)
- [EasyFig](https://mjsull.github.io/Easyfig/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/easyfig.png)
- [EvolutionHighway](http://eh-demo.ncsa.illinois.edu/) (The 'evolutionary
highway' image type is reproduced in some other packages e.g.
https://github.com/marta-fb/syntenyPlotteR, paper
https://doi.org/10.1126/science.1111387)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/evolutionaryhighway.jpg)
- [FastANI](https://github.com/ParBLiSS/FastANI)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/fastani.jpg)
- [GBrowse_syn](http://gmod.org/wiki/GBrowse_syn)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gbrowse_syn.png)
- [GCSnap](https://github.com/JoanaMPereira/GCsnap)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gcsnap.png)
- [GENESPACE](https://github.com/jtlovell/GENESPACE/) (Includes a powerful
analysis pipeline, worth reading the paper)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genespace.png)
- [Genome Context Viewer](https://www.legumefederation.org/gcv/phytozome_10_2/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome_context_viewer.png)
- [Genome-plots-processing](https://github.com/filip-husnik/genome-plots-processing)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome_plots_processing.png)
- [GenomeMatcher](http://www.ige.tohoku.ac.jp/joho/gmProject/gmmanual.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomematcher.png)
- [GenomeSyn](https://github.com/jmsong2/GenomeSyn)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomesyn.png)
- [GenomicBreaks](https://oist.github.io/GenomicBreaks/articles/GenomicBreaks.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomicbreaks.png)
- [Genomicus](https://www.genomicus.biologie.ens.fr/genomicus/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomicus.png)
- [gggenomes](https://github.com/thackl/gggenomes)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gggenomes.png)
- [GGisy](https://github.com/Sanrrone/GGisy)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggisy.png)
- [GIVE](https://zhong-lab-ucsd.github.io/GIVE_homepage/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/give_hic.png)
- [GSSPlayground](https://github.com/orangeSi/GSSplayground)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gssplayground.png)
- [JAX Synteny browser](https://github.com/TheJacksonLaboratory/syntenybrowser)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jax_synteny_browser.png)
- [LinearDisplay.pl](https://github.com/JCVenterInstitute/LinearDisplay) (readme
says to cite this paper)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/lineardisplay.png)
- [mauve-viewer](https://github.com/nconrad/mauve-viewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mauve_viewer.png)
- [MCScan (python version)]()
(Also has 2024 citation here
https://onlinelibrary.wiley.com/doi/10.1002/imt2.211)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcscan_python.png)
- [MCScanX](https://github.com/wyp1125/MCScanX)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcscanx.png)
- [mGSV (multiple genome synteny viewer)](https://github.com/kashmatic/mGSV)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mgsv.jpg)
- [miropeats](http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/)
(image from 2021 paper
https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/miropeats.png)
- [MizBee](http://www.cs.utah.edu/~miriah/mizbee/Overview.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mizbee.jpg)
- [ModDotPlot](https://github.com/marbl/ModDotPlot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/moddotplot.png)
- [multiGenomicContext](https://github.com/Sanrrone/multiGenomicContext)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/multicontext.png)
- [Multiple genome viewer](http://www.informatics.jax.org/mgv/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mgv.png)
- [NCBI CGV](https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/05/cgv-beta-release/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgv.png)
- [NGenomeSyn](https://github.com/hewm2008/NGenomeSyn) (See also RectChr)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ngenomesyn.png)
- [ntSynt](https://github.com/bcgsc/ntSynt/tree/main/visualization_scripts)
(Uses gggenomes)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ntsynt.png)
- [odp (oxford dot plots)](https://github.com/conchoecia/odp) (Pub is not for
visualization tool, but it is suggested to cite this paper)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/odp.png)
- [OMA local synteny browser](https://omabrowser.org/oma/synteny/ADH1A_HUMAN/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/oma.png)
- [pafr](https://github.com/dwinter/pafr)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pafr.png)
- [Parasight](https://baileylab.brown.edu/parasight/galframe.html) (Examples at
https://ratparalogy.gs.washington.edu/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/parasight.png)
- [PipMaker](http://pipmaker.bx.psu.edu/pipmaker/) (See also MultiPipMaker
http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pipmaker.png)
- [plotsr](https://github.com/schneebergerlab/plotsr) (see also
https://github.com/schneebergerlab/syri)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotsr.png)
- [pretzel](https://github.com/plantinformatics/pretzel)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pretzel.png)
- [progressiveMauve viewer](http://darlinglab.org/mauve/user-guide/viewer.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/progressive_mauve.png)
- [PSAT](http://www.nwrce.org/psat)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/psat.png)
- [pyGenomeViz](https://github.com/moshi4/pyGenomeViz) (See also
https://github.com/moshi4/MGCplotter https://github.com/moshi4/GBKviz
https://github.com/moshi4/plot_genome_align_fig)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygenomeviz.png)
- [r2cat](https://github.com/phuseman/r2cat)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/r2cat.jpeg)
- [RectChr](https://github.com/BGI-shenzhen/RectChr)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rectchr.png)
- [SafFire](https://mrvollger.github.io/SafFire/#ref=CHM13_v1.1&query=GRCh38)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/saffire.png)
- [SequenceSurveyor](https://graphics.cs.wisc.edu/Vis/SequenceSurveyor/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequencesurveyor.png)
- [ShinySyn](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/shinysyn.png)
- [SimpleSynteny](https://www.dveltri.com/simplesynteny/about.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/simplesynteny.jpg)
- [Smash++](https://github.com/smortezah/smashpp)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/smashpp.png)
- [Sybil](http://sybil.sourceforge.net/) (Download
https://sourceforge.net/projects/sybil/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sybil.png)
- [SyMap](http://www.agcol.arizona.edu/software/symap/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/symap.png)
- [SynBrowse](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/synbrowse.png)
- [Synima](https://github.com/rhysf/Synima)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/synima.png)
- [syntenyPlotteR](https://github.com/marta-fb/syntenyPlotteR)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntenyplotter.png)
- [SyntenyPortal](http://bioinfo.konkuk.ac.kr/synteny_portal/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntenyportal.png)
- [syntR](https://www.samuklab.com/syntR/articles/syntr_tutorial.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntr.png)
- [SynTView](http://hub18.hosting.pasteur.fr/SynTView/documentation/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntview.png)
- [SynVisio](https://synvisio.github.io/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/synvisio.png)
- [SYNY](https://github.com/PombertLab/SYNY)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syny.png)
- [TNA](https://github.com/martinghunt/tna) (ACT (Artemis Comparison Tool)
replacement)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tna.png)
- [TreeBrowser (MicrobesOnline)](http://www.microbesonline.org/cgi-bin/treeBrowse.cgi?locus=17761)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/treegenome.png)
- [Tripal MapViewer](https://github.com/statonlab/tripal_map)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tripal_mapviewer.png)
- [VISTA browser](http://pipeline.lbl.gov/cgi-bin/gateway2)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vista.png)
- [WGDI](https://github.com/SunPengChuan/wgdi)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wgdi.png)
- [XMatchView](https://www.bcgsc.ca/resources/software/xmatchview)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/xmatchview.png)
## Coverage
- [BAMdash](https://github.com/jonas-fuchs/BAMdash/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamdash.png)
- [dep](https://github.com/slw287r/dep) (Can handle very deep coverage)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dep.png)
- [ggcoverage](https://cran.r-project.org/web/packages/ggcoverage/vignettes/ggcoverage.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggcoverage.png)
- [SeqCover](https://brentp.github.io/seqcover/#gene=AIFM1)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqcover.png)
- [signac](https://github.com/timoast/signac/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/signac.png)
- [Trackplot (R)](https://github.com/PoisonAlien/trackplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackplot.png)
- [wiggleplotr](http://bioconductor.org/packages/devel/bioc/vignettes/wiggleplotr/inst/doc/wiggleplotr.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wiggleplotr.png)
## Deadlink
- [CGH-Explorer](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cghexplorer.jpg)
- [DNAVis](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnavis.png)
- [VAMP](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vamp.jpg)
## Dotplot
- [D-GENIES](http://dgenies.toulouse.inra.fr/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dgenies.png)
- [DAGchainer](http://dagchainer.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dagchainer.png)
- [Delly-maze](https://github.com/dellytools/maze) (see also
https://www.gear-genomics.com/maze/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/maze.png)
- [Discoplot](https://github.com/mjsull/DiscoPlot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/discoplot.png)
- [Dot](https://dot.sandbox.bio/) (Python data preparation script)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dot.png)
- [Dotlet](https://dotlet.vital-it.ch/) (The original publication was 2000 but
updated ~2020 with reactjs)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotlet.png)
- [Dotplot (chirimoyo)](https://chirimoyo.ac.uma.es/bitlab/portfolio/dotplot/)
- [dotPlotly](https://github.com/tpoorten/dotPlotly/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotplotly.png)
- [Dotter](https://sonnhammer.sbc.su.se/Dotter.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotter.png)
- [Dottup](https://www.bioinformatics.nl/cgi-bin/emboss/help/dottup) (also seen
here
http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dottup.png)
- [FlexiDot](https://github.com/molbio-dresden/flexidot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/flexidot.png)
- [Gepard](http://cube.univie.ac.at/gepard)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gepard.jpeg)
- [ggplot2 mummerplot](https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummerplot_ggplot2.png)
- [iLambda/Dotplot](https://github.com/iLambda/dotplot)
- [Jdot](https://github.com/LyonsLab/jdot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jdot.png)
- [JGI/IMG](https://img.jgi.doe.gov/) (Dotplot use MUMmer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jgiimg.png)
- [last-dotplot](https://gitlab.com/mcfrith/last)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/last_dotplot.png)
- [local-rearrangements](https://github.com/mcfrith/local-rearrangements) (Can
color dotplots with annotations for e.g. exons, transposons, low complexity
regions. See also last-dotplot. Nice figure using it here
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00762-1/figures/4)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/local-rearrangements.png)
- [MashMap](https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mashmap.png)
- [mcutils](https://github.com/mchaisso/mcutils)
(https://twitter.com/mjpchaisson/status/1040363992206569472)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcutils_dotplot.jpeg)
- [Minidot](https://github.com/thackl/minidot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/minidot.png)
- [Mummer-idotplot](https://github.com/ryought/mummer-idotplot)
- [Mummerplot](http://mummer.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummerplot.png)
- [oxford-plots](https://github.com/jherrero/oxford-plots) (Has nice description
of a synteny pipeline here
https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/oxford.png)
- [Redotable](https://github.com/s-andrews/redotable)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/redotable.png)
- [shinyChromosome](http://150.109.59.144:3838/shinyChromosome/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/shinychromosome.png)
- [syntenyPlotByR](https://github.com/shingocat/syntenyPlotByR)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/synteny_plot_by_r.png)
## Epigenomics
- [Chip Monk](http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/) (Also
see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chipmonk.png)
- [Chipster](https://chipster.csc.fi/) (Copy number tutorial
https://chipster.csc.fi/manual/cn-tutorial.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chipster.jpg)
- [cisGenome Browser](https://jhui2014.github.io/browser/screenshots.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cisgenome.png)
- [CoolBox](https://github.com/GangCaoLab/CoolBox) (fork of pyGenomeTracks)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/coolbox.png)
- [EaSeq](https://easeq.net/screenshots/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/easeq.png)
- [Epilogos](https://epilogos.altius.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/epilogos.jpg)
- [Epiviz](https://epiviz.github.io/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/epiviz.png)
- [HiPiler](http://hipiler.higlass.io)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/hipiler.png)
- [JBR](https://artyomovlab.wustl.edu/jbr/2018_h3k27ac_aging/) (Not open source,
at least not on github)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbr.png)
- [Juicebox](https://github.com/aidenlab/Juicebox)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/juicebox.jpg)
- [Juicebox.js](http://www.igv.org/doc/juiceboxjs.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/juiceboxjs.jpg)
- [Peax](https://github.com/Novartis/peax)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/peax.png)
- [python-genome-browser aka pygbrowse](https://github.com/phageghost/python-genome-browser/blob/master/pygbrowse_demonstration.ipynb)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygbrowse.png)
## Exotic
- [BigTop](https://blog.dnanexus.com/2019-05-21-bigtop-data-visualization/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bigtop.png)
- [Cylindrical alignment app](https://sourceforge.net/projects/cylindrical-alignment-app/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cylindrical_alignment_viewer.png)
- [DNASkittle](https://www.dnaskittle.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaskittle.png)
- [FluentDNA](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203487/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/fluentdna.jpeg)
- [sockeye](https://www.bcgsc.ca/resources/software/sockeye)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sockeye.jpg)
- [spinteny](https://github.com/skinner/spinteny)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/spinteny.png)
## Expression
- [GTEX Locus browser](https://gtexportal.org/home/locusBrowserPage/ACTN3)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtex_locus.png)
## Gene fusion
- [AGFusion](https://github.com/murphycj/AGFusion) (See also
https://www.agfusion.app/ for web based version)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/agfusion.png)
- [arriba](https://github.com/suhrig/arriba)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/arriba.png)
- [Chimeraviz](https://github.com/stianlagstad/chimeraviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chimeraviz.png)
- [clinker (gene fusion software)](https://github.com/Oshlack/Clinker/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/clinker_fusion.png)
- [FusionInspector](https://github.com/FusionInspector/FusionInspector/wiki)
(Uses igv.js)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/fusioninspector.png)
- [GeneFuse](https://opengene.org/GeneFuse/report.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genefuse.png)
- [MAVIS](http://mavis.bcgsc.ca/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mavis.png)
## Gene structure
- [Apollo aka WebApollo](https://genomearchitect.readthedocs.io/en/latest/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/webapollo.jpg)
- [D3GB](http://d3gb.usal.es/) (Live link
http://d3gb.usal.es/docs/HumanGenomeBrowser/index.html?r=12:121113963-121213963
doesn't work anymore)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/d3gb.png)
- [ggtranscript](https://github.com/dzhang32/ggtranscript)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggtranscript.png)
- [TnT](https://tnt.marlin.pub/articles/introduction)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tnt.png)
## Graph
- [AGB assembly graph browser](https://github.com/almiheenko/AGB)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/agb.jpeg)
- [Bandage](https://github.com/rrwick/Bandage/) (See also BandageNG
https://github.com/asl/BandageNG)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bandage.png)
- [ctag](https://github.com/AbeelLab/ctag) (See also hygene
https://github.com/ProgrammingLife2017/hygene)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ctag.png)
- [gfaestus](https://github.com/chfi/gfaestus) (See demo video displaying GFF3
annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gfaestus.png)
- [GfaViz](https://github.com/ggonnella/gfaviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gfaviz.png)
- [graphgenomeviewer](https://cmdcolin.github.io/graphgenomeviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/graphgenomeviewer.png)
- [IGGE](https://github.com/immersivegraphgenomeexplorer/IGGE) (Not open source)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/igge.png)
- [LINX](https://github.com/hartwigmedical/hmftools/tree/master/linx) (part of
the PURPLE/GRIDSS/LINX pipeline)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/linx.png)
- [MoMi-G](https://github.com/MoMI-G/MoMI-G)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/momig.png)
- [odgi draw + odgi viz + odgi inject](https://odgi.readthedocs.io/en/latest/index.html)
(Example from https://github.com/pangenome/pggb, see also gene arrow map
https://odgi.readthedocs.io/en/latest/rst/tutorials/injecting_gene_arrows.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/odgi.png)
- [panGraphViewer](https://github.com/TF-Chan-Lab/panGraphViewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pangraphviewer.jpg)
- [PGR-TK](https://github.com/cschin/pgr-tk)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgrtk.png)
- [pgv (graph tool)](https://w-gao.github.io/pgv/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgv2.png)
- [sequence tube map](https://github.com/vgteam/sequenceTubeMap)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequence_tube_map.png)
- [SGTK (scaffold graph toolkit)](https://olga24912.github.io/SGTK/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sgtk.png)
- [Shasta](https://chanzuckerberg.github.io/shasta/ComputationalMethods.html#ReadGraph)
(Uses graphviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/shasta.png)
- [strangepg](https://github.com/qwx9/strangepg)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/strangepg.png)
- [VAG](https://github.com/lipingfangs/VAG)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vag.jpg)
- [VRPG](https://github.com/codeatcg/VRPG)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vrpg.png)
- [waragraph](https://chfi.github.io/waragraph/) (Deployed to the web via wasm)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/waragraph.png)
## GWAS
- [CMPlot](https://github.com/YinLiLin/CMplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cmplot.png)
- [GeneticsMakie.jl](https://github.com/mmkim1210/GeneticsMakie.jl)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneticsmakie.png)
- [ggplot2 manhattan plot](https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/)
(This is not a preconfigured tool but a blog post tutorial with tidy data and
ggplot2)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggplot2_manhattan.png)
- [LDBlockShow](https://github.com/BGI-shenzhen/LDBlockShow)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ldblockshow.png)
- [Locuszoom](http://locuszoom.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/locuszoom.png)
- [PureScript genetics browser](https://github.com/chfi/purescript-genetics-browser)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/purescript.png)
## Heatmap
- [UCSC Xena](https://xena.ucsc.edu/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/xena.png)
- [VIVA](https://www.biorxiv.org/content/10.1101/589879v1.full.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/viva.png)
## Hi-C
- [figeno](https://github.com/CompEpigen/figeno)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/figeno.png)
- [gcMapExplorer](https://github.com/rjdkmr/gcMapExplorer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gcmapexplorer.png)
- [Plotgardener](https://github.com/PhanstielLab/plotgardener/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotgardener.png)
- [PretextView](https://github.com/wtsi-hpag/PretextView)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pretextview.jpg)
## Historical
- [Apollo](https://web.archive.org/web/20060927154956/http://www.fruitfly.org/annot/apollo/)
(URL is an archive.org link)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/apollo.jpg)
- [gff2ps](https://genome.crg.es/software/gfftools/GFF2PS.html) (Used to make
original figures for the human Celera genome)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gff2ps.png)
- [Internet Contig Explorer](https://www.bcgsc.ca/resources/software/ice)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/internet_contig_explorer.jpg)
## Ideogram
- [chromPlot](https://www.bioconductor.org/packages/release/bioc/vignettes/chromPlot/inst/doc/chromPlot.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromplot.png)
- [chrov](https://github.com/rraadd88/chrov) (See also usage in
https://github.com/rraadd88/beditor)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chrov.png)
- [eweitz/Ideogram](https://github.com/eweitz/ideogram)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/eweitz_ideogram.png)
- [ezcharts](https://github.com/epi2me-labs/ezcharts)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ezcharts.png)
- [Flash Gviewer](http://gmod.org/wiki/Flashgviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/flashgviewer.png)
- [genomegraphs](http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomegraphs.png)
- [Ideogram](https://github.com/RCollins13/HumanIdiogramLibrary)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rcollins_ideogram.png)
- [Ideogram viewer](https://bioinformatics.mdanderson.org/public-software/ideogramviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ideogramviewer.png)
- [Ideoplot](https://github.com/mchaisso/Ideoplot)
- [IdeoViz](https://www.bioconductor.org/packages/release/bioc/vignettes/IdeoViz/inst/doc/Vignette.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ideoviz.png)
- [karyoploteR](https://github.com/bernatgel/karyoploteR)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/karyoploter.png)
- [KaryotypeSVG](https://github.com/andreasprlic/karyotypeSVG)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/karyotypesvg.png)
- [NCBI Genome Decoration](undefined) (Was located at
https://www.ncbi.nlm.nih.gov/genome/tools/gdp/, sunsetted in 2023)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ncbi_genome_decoration.png)
- [PhenoGram](https://ritchielab.org/software/phenogram-downloads) (Can be web
server or download)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/phenogram.png)
- [RIdeogram](https://github.com/TickingClock1992/RIdeogram)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rideogram.png)
- [tagore](https://github.com/jordanlab/tagore)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tagore.png)
- [UCSC Genome Graphs](http://genome.ucsc.edu/cgi-bin/hgGenome)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ucsc_genome_graph.png)
## K-mer
- [Panagram](https://github.com/kjenike/panagram)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/panagram.png)
## Linear
- [Gnomad browser](https://github.com/macarthur-lab/gnomadjs)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gnomad.png)
## Local ancestry
- [fineSTRUCTURE aka ChromoPainter](http://www.paintmychromosomes.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/finestructure.png)
- [MOSAIC](https://maths.ucd.ie/~mst/MOSAIC/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mosaic.png)
- [winpca](https://github.com/MoritzBlumer/winpca)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/winpca.png)
## Logo
- [LogoJS](https://logojs.wenglab.org/app/gallery/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/logojs.png)
## Long reads
- [methylartist](https://github.com/adamewing/methylartist)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/methylartist.png)
## Manhattan
- [locuszoomr](https://cran.r-project.org/web/packages/locuszoomr/vignettes/locuszoomr.html)
(See also easylabel for manhattan plots
https://cran.r-project.org/web/packages/easylabel/vignettes/easylabel.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/locuszoomr.jpg)
- [topr](https://github.com/totajuliusd/topr/) (Includes locuszoom style plot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/topr.png)
## Methylation
- [AnnoJ](https://brainome.ucsd.edu/howto_annoj.html) (See list of instances of
the browser here https://ecker.salk.edu/genome-browser/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/annoj.png)
- [modbamtools](https://github.com/rrazaghi/modbamtools)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/modbamtools.png)
- [NanoMethViz](http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/nanomethviz.png)
## Microbiology
- [clonifier](https://dlesl.github.io/clonifier/) (per github: 'A web app for
viewing plasmid maps & genomes, and simulating PCR and Gibson assembly')
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/clonifier.png)
- [Edinburgh-Genome-Foundry/DnaFeaturesViewer](https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer)
(See also https://github.com/Edinburgh-Genome-Foundry/Caravagene)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnafeaturesviewer.png)
- [GECO](http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/geco.png)
- [GeCoViz](https://gecoviz.cgmlab.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gecoviz.png)
- [GeneViTo](http://athina.biol.uoa.gr/bioinformatics/GENEVITO/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genevito.jpg)
- [IslandViewer and IslandPlot](https://bl.ocks.org/lairdm/c6c235dbfa6e6ee61565)
(web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/islandplot.png)
- [lovis4u](https://github.com/art-egorov/lovis4u)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/lovis4u.png)
## Mobile app
- [iGenomics](https://github.com/stuckinaboot/iGenomics)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/igenomics.png)
## MSA
- [AA (alignment annotator)](http://www.bioinformatics.org/strap/aa) (also see
STRAP) [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aa.png)
- [abrowse (MSA viewer)](https://github.com/ihh/abrowse)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/abrowse.png)
- [alen](https://github.com/jakobnissen/alen)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alen.png)
- [alignfigR](https://cran.r-project.org/web/packages/alignfigR/vignettes/my-vignette.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignfigr.png)
- [alignment.js](https://github.com/veg/alignment.js)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentjs.png)
- [AlignmentComparator](http://bioinfweb.info/AlignmentComparator/) (Uses
http://bioinfweb.info/LibrAlign/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentcomparator.png)
- [AlignmentViewer](https://alignmentviewer.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentviewer.png)
- [AliTreeViz](https://www.npmjs.com/package/alitreeviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alitreeviz.png)
- [AliView](http://www.ormbunkar.se/aliview/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/aliview.png)
- [ALVIS (MSA viewer)](https://www.ebi.ac.uk/research/goldman/software/alvis)
(Introduces sequence bundles concept, also see web app version
https://www.ebi.ac.uk/goldman-srv/sequencebundles/ source code
https://bitbucket.org/schwarzlab/alvis/src/master/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alvis.png)
- [BioJS/MSA](https://msa.biojs.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/biojsmsa.png)
- [Boxshade](https://embnet.vital-it.ch/software/BOX_form.html) (Also available
as a command line tool with `apt install boxshade`. See also rMSA which can
automate running boxshade from within R)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/boxshade.png)
- [CIAlign](https://github.com/KatyBrown/CIAlign) (Has useful utility functions
to clean gaps and trim MSAs)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cialign.png)
- [CView](https://sourceforge.net/projects/cview/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cview.png)
- [ESPript](http://espript.ibcp.fr/ESPript/ESPript/) (Primarily a web interface
but can download a binary for linux
https://espript.ibcp.fr/ESPript/ESPript/esp_faq.php)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/espript.png)
- [ete](http://etetoolkit.org/gallery/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ete.png)
- [ggmsa](http://yulab-smu.top/ggmsa/) (See also ggtree)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggmsa.png)
- [ggtree](https://github.com/YuLab-SMU/ggtree) (see
https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA
example)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggtree.png)
- [Jalview](https://www.jalview.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jalview.jpg)
- [JSAV](http://www.bioinf.org.uk/software/jsav)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jsav.png)
- [MEGA-X](https://www.megasoftware.net/) (original paper from 1994 but actively
updated. requires EULA for download)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/megax.png)
- [MSABrowser](https://thekaplanlab.github.io/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/msabrowser.png)
- [msaR](https://github.com/zachcp/msaR) (uses BioJS/MSA)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/msar.png)
- [MView](https://www.ebi.ac.uk/Tools/msa/mview/) (See also their web versions
of clustal omega etc. which have similar outputs)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mview.png)
- [NCBI MSA Viewer](https://www.ncbi.nlm.nih.gov/projects/msaviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ncbimsa.png)
- [ProViz](http://slim.icr.ac.uk/proviz/index.php) (See also alphafold
visualization as tracks
http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/proviz.png)
- [pyBoxshade](https://github.com/mdbaron42/pyBoxshade) (also see boxshade)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pyboxshade.png)
- [pymsaplotter](https://github.com/orangeSi/pymsaploter)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pymsaplotter.png)
- [React MSAViewer](https://github.com/plotly/react-msa-viewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/react-msa-viewer.png)
- [react-msaview](https://github.com/GMOD/react-msaview)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/react-msaview.png)
- [rMSA](https://github.com/mhahsler/rMSA/blob/master/vignettes/rMSA_vignette.pdf)
(Can automate boxshade)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rmsa.png)
- [Seaview](http://doua.prabi.fr/software/seaview)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seaview.png)
- [seqotron](https://github.com/4ment/seqotron)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqotron.png)
- [seqvisr](https://github.com/vragh/seqvisr/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqvisr.png)
- [SNIPViz](http://www.yeastrc.org/snipviz/4.HTML_Config_retrieve_newick_and_fasta_from_server/snip_viz_HTML_config_with_newick_clustering.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpviz.png)
- [STRAP](http://www.bioinformatics.org/strap/) (also see AA)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/strap.png)
- [TeXShade](http://mirrors.ibiblio.org/CTAN/macros/latex/contrib/texshade/texshade.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/texshade.png)
- [Wasabi](http://wasabiapp.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wasabi.png)
## Multi-way synteny
- [Mumemto](https://github.com/vikshiv/mumemto)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mumemto.png)
- [SVbyEye](https://htmlpreview.github.io/?https://github.com/daewoooo/SVbyEye/blob/master/man/doc/SVbyEye.html)
(AKA plotAVA)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svbyeye.png)
## Pangenome
- [Pan-Tetris](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pantetris.png)
- [Panacaea](https://github.com/JCVenterInstitute/PanACEA)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/panacaea.png)
- [Panache](https://github.com/SouthGreenPlatform/panache)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/panache.png)
- [panX](http://pangenome.tuebingen.mpg.de/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/panx.jpeg)
- [PGAP-X](https://pgapx.zhaopage.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgapx.png)
- [PGV (pangenome tool)](https://github.com/ucrbioinfo/PGV)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgv1.png)
- [Phandango](https://jameshadfield.github.io/phandango/#/examples)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/phandango.png)
- [RPAN (3kricedb)](http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rpan.png)
- [TASUKE](https://ricegenome.dna.affrc.go.jp/) (info about multi-genome-browser
https://tasuke.dna.affrc.go.jp/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tasuke.png)
## Phylogenetics
- [Gingr](https://harvest.readthedocs.io/en/latest/content/gingr.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gingr.png)
- [Nextclade](https://clades.nextstrain.org/) (Related usage on nextstrain app
also)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/nextclade.png)
- [Taxonium](https://taxonium.org) (Genome variation visualisation in Taxonium
is provided by the 'Treenome Viewer':
https://academic.oup.com/bioinformatics/article/39/1/btac772/6858450)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/taxonium.png)
## Population
- [GWAS catalog browser](https://www.ebi.ac.uk/gwas/variants/rs1558902)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gwascatalog.png)
- [Haploview](https://www.broadinstitute.org/haploview/haploview)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/haploview.png)
- [Human genome dating](https://human.genome.dating/region/chr1_13250000) (made
with vega/d3)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/human_genome_dating.png)
- [Panoptes](https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/panoptes.png)
- [pixy](https://pixy.readthedocs.io/en/latest/plotting.html#a-genome-wide-plot-of-summary-statistics)
(The link in readthedocs shows a nice general purpose way to plot
multi-chromosome plots in ggplot2 with facet grid. Alternative methods for
multi-chromosome plots shown by the manhattan ggplot2 tutorial
(https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/ uses
cumulative bp instead of facet_grid))
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pixy.png)
- [PopSV](https://github.com/jmonlong/PopSV/blob/master/3-Visualization.md)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/popsv.png)
- [SWAV](http://swav.popgenetics.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/swav.png)
- [vcfR](https://knausb.github.io/vcfR_documentation/) (image shows chromoqc
output)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcfr.png)
## Protein
- [Aquaria](http://aquaria.ws/Q9HD67/5i0i/A)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/aquaria.png)
- [drawProteins](https://github.com/brennanpincardiff/drawProteins)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/drawprotein.png)
- [IBS (Illustrator for Biological Sequences)](http://ibs.biocuckoo.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ibs.jpg)
- [nightingale/protvista](https://ebi-webcomponents.github.io/nightingale/#/msa)
(Used on InterProScan website https://www.ebi.ac.uk/interpro/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/nightingale.png)
- [PFAM generate_graphic](https://pfam.xfam.org/generate_graphic) (Also see
guide here https://pfam.xfam.org/help#tabview=tab10)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pfam.png)
- [Prosite/MyDomains](https://prosite.expasy.org/mydomains)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/prosite.png)
- [Protael](http://sanshu.github.io/protaelweb/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/protael.png)
- [ProteinPaint](https://pecan.stjude.cloud/proteinpaint)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/proteinpaint.png)
- [pViz](https://github.com/Genentech/pviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pviz.jpg)
- [TogoStanza Protein Browser](https://db-dev.jpostdb.org/ts/stanza/protein_browser/help.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/togostanza.png)
## Quantitative
- [wasm bigwig demo browser](https://shk656461.github.io/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wasm_bigwig.png)
## Repeats
- [GraphAlignmentViewer](https://github.com/Illumina/GraphAlignmentViewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/graphalignmentviewer.png)
- [REPAVER](https://gitlab.com/gringer/bioinfscripts/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/repaver.jpg)
- [REViewer](https://github.com/Illumina/REViewer) (See also
GraphAlignmentViewer, similar look and from illumina also)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/reviewer.png)
- [SODA](https://sodaviz.org/) (Describes itself as a low-level library to
create larger applications with)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/soda.png)
- [StainedGlass](https://github.com/mrvollger/StainedGlass)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/stainedglass.png)
- [TRVZ (TRGT tandem repeat genotyping visualizer)](https://github.com/PacificBiosciences/trgt)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/trvz.png)
## Single cell
- [ArchR](https://www.archrproject.com/articles/Articles/tutorial.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/archr.png)
- [casper](https://github.com/akdess/CaSpER)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/casper.png)
- [copykat](https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/copykat.png)
- [gingko](http://qb.cshl.edu/ginkgo/?q=/9EiUttUP0CBHs3WnuBa0)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gingko.jpeg)
- [Millefy](https://github.com/yuifu/millefy)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/millefy.png)
- [MosaicCatcher pipeline](https://github.com/friendsofstrandseq/mosaicatcher-pipeline)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mosaicatcher.png)
- [numbat](https://kharchenkolab.github.io/numbat/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/numbat.png)
- [scCNV_heatmap](https://github.com/StefanKurtenbach/scCNV_heatmap)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sccnv_heatmap.png)
## Special-purpose
- [SEQing](https://github.com/malewins/SEQing)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqing.png)
- [UGENE](http://ugene.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ugene.png)
## Splicing
- [Slinker](https://github.com/Oshlack/Slinker) (See also, clinker (gene fusion
software))
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/slinker.png)
- [splicejam](https://github.com/jmw86069/splicejam)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/splicejam.png)
- [Vials](http://vials.io/)
## Static
- [BAMSnap](https://github.com/parklab/bamsnap)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamsnap.png)
- [bcftools roh](https://samtools.github.io/bcftools/howtos/roh-calling.html)
(Plots runs of homozygosity, has interactive plot-roh.py helper too)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bcftools_roh.png)
- [cgplot](https://github.com/dfguan/cgplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgplot.png)
- [ChIA-Pipe](https://github.com/TheJacksonLaboratory/ChIA-PIPE)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chiapipe.png)
- [CNView](https://github.com/RCollins13/CNView)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnview.jpg)
- [CNVPlot](https://github.com/dantaki/CNVplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvplot.jpg)
- [CNVpytor](https://github.com/abyzovlab/CNVpytor)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvpytor.png)
- [DNAPlotLib](https://github.com/VoigtLab/dnaplotlib)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaplotlib.png)
- [ExonIntron](http://wormweb.org/exonintron)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/exonintron.png)
- [FeatureViewer](https://github.com/calipho-sib/feature-viewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/featureviewer.png)
- [geneviewer](https://nvelden.github.io/geneviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneviewer.png)
- [Geneviz](https://jrderuiter.github.io/geneviz/usage.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneviz.png)
- [Genome STRiP](http://software.broadinstitute.org/software/genomestrip/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomestrip.png)
- [GenomeTools](http://genometools.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genometools.png)
- [GenomeView](https://github.com/nspies/genomeview)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeview.png)
- [genoPlotR](http://genoplotr.r-forge.r-project.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genoplotr.png)
- [ggbio](http://www.bioconductor.org/packages/2.11/bioc/vignettes/ggbio/inst/doc/ggbio.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggbio.png)
- [GGgenes](https://github.com/wilkox/gggenes)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gggenes.png)
- [GGsashimi](https://github.com/guigolab/ggsashimi)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggsashimi.png)
- [gtrellis](http://bioconductor.org/packages/devel/bioc/vignettes/gtrellis/inst/doc/gtrellis.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtrellis.png)
- [Gviz](https://bioconductor.org/packages/release/bioc/html/Gviz.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gviz.png)
- [Hagfish](https://github.com/mfiers/hagfish/wiki/Plots)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/hagfish.png)
- [HiCPlotter](https://github.com/kcakdemir/HiCPlotter)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/hicplotter.jpg)
- [JVarKit/BamToSVG](http://lindenb.github.io/jvarkit/BamToSVG.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamtosvg.jpg)
- [Lollipops](https://github.com/joiningdata/lollipops)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/lollipops.png)
- [Mason](http://www.yeastrc.org/mason/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mason.png)
- [Methplotlib](https://github.com/wdecoster/methplotlib)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/methplotlib.jpg)
- [mummer2circos](https://github.com/metagenlab/mummer2circos)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummer2circos.png)
- [Pairoscope](http://pairoscope.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pairoscope.png)
- [pauvre](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991124/figure/fig-3/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pauvre.png)
- [pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks) (See also
https://pypi.org/project/gtracks/ which is a separate project that is powered
by pyGenomeTracks)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygenometracks.png)
- [RACER](https://oliviasabik.github.io/RACERweb/articles/IntroToRACER.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/racer.png)
- [RepViz](https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4473-z)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/repviz.png)
- [Samplot](https://github.com/ryanlayer/samplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/samplot.jpg)
- [SashimiPlot](https://miso.readthedocs.io/en/fastmiso/sashimi.html) (See also
rmats2sashimiplot which uses MISO. MATS stands for Multivariate Analysis of
Transcript Splicing)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sashimi-plot-example.png)
- [shabam](https://github.com/dlrice/shabam)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/shabam.png)
- [SparK](https://github.com/harbourlab/SparK)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/spark.png)
- [Spliceclust](https://github.com/pkimes/spliceclust)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/spliceclust.png)
- [Sushi](https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sushi.png)
- [svist4get](https://link.springer.com/article/10.1186/s12859-019-2706-8)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svis4get.png)
- [svv](https://github.com/ryanlayer/svv)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svv.png)
- [svviz](https://github.com/svviz/svviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svviz.png)
- [svviz2](https://github.com/nspies/svviz2)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svviz2.png)
- [trackViewer](https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackviewer.png)
## SV
- [AmpliconArchitect](https://github.com/virajbdeshpande/AmpliconArchitect) (The
term amplicon refers essentially to extrachromosomal DNA in cancer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ampliconarchitect.png)
- [asgart](https://github.com/delehef/asgart)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/asgart.png)
- [bigly](https://github.com/brentp/bigly)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bigly.png)
- [gGnomes](https://github.com/mskilab/gGnome)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggnomesr.png)
- [gGnomes.js](https://github.com/mskilab/gGnome.js)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggnomes.png)
- [Gremlin](http://compbio.cs.brown.edu/projects/gremlin/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gremlin.png)
- [InGAP-SV](http://ingap.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ingap_sv.png)
- [Introgression browser](https://git.wageningenur.nl/aflit001/ibrowser)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/introgression_browser.png)
- [NeoLoopFinder](https://github.com/XiaoTaoWang/NeoLoopFinder)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/neoloopfinder.png)
- [ReConPlot](https://github.com/cortes-ciriano-lab/ReConPlot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/reconplot.png)
- [Ribbon](http://genomeribbon.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeribbon.png)
- [SMRT View](http://files.pacb.com/software/smrtanalysis/2.3.0/doc/smrtview/help/Webhelp/App_View_Epipro.htm)
(wiki page https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/smrtview.png)
- [SplitThreader](http://splitthreader.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/splitthreader.png)
- [SVhawkeye](https://github.com/yywan0913/SVhawkeye)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svhawkeye.jpg)
- [SVPV](https://github.com/VCCRI/SVPV)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svpv.jpg)
- [vcf2circos](https://github.com/bioinfo-chru-strasbourg/vcf2circos) (Based on
PCircos https://github.com/CJinny/PCircos)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcf2circos.png)
## Synthetic biology
- [ApE (a plasmid editor)](https://jorgensen.biology.utah.edu/wayned/ape/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/aplasmideditor.png)
- [Chopchop](http://chopchop.cbu.uib.no/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chopchop.png)
- [plascad](https://github.com/David-OConnor/plascad)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plascad.png)
- [plasmapR](https://github.com/BradyAJohnston/plasmapR)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plasmapr.png)
- [seqviz](https://github.com/Lattice-Automation/seqviz#viewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqviz.png)
## Text based
- [Alan](https://github.com/mpdunne/alan)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alan.png)
- [Alv](https://github.com/arvestad/alv)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alv.png)
- [ASCIIGenome](https://github.com/dariober/ASCIIGenome)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/asciigenome.png)
- [Bamcov](https://github.com/fbreitwieser/bamcov)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamcov.png)
- [BLAST+ (reading -outfmt 0 pairwise output is the original CLI bioinformatics!)](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
- [Hapviz](https://github.com/ekg/hapviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/hapviz.png)
- [pileuppy](https://gitlab.com/tprodanov/pileuppy)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pileuppy.png)
- [plotReads](http://campuspress.yale.edu/knightlab/ruddle/plotreads/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotreads.png)
- [rich-msa](https://github.com/althonos/rich-msa)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/richmsa.png)
- [Rna Alignment Viewers (Colorstock, SScolor, Ratón)](http://biowiki.org/wiki/index.php?title=Rna_Alignment_Viewers&redirect=no)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rnaalignment.png)
- [Sam2pairwise](https://github.com/mlafave/sam2pairwise)
- [Samtools depth visualization](https://twitter.com/yokofakun/status/1178686978541441025)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/depthplot.png)
- [Samtools tview](http://www.htslib.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tview.png)
- [SvABA](https://github.com/walaj/svaba#alignmentstxtgz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svaba.png)
- [VizAln (from HipSTR)](https://github.com/tfwillems/HipSTR)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/hipstr.png)
- [wgatools](https://github.com/wjwei-handsome/wgatools)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wgatools.png)
## Transposons
- [TE-nest](https://github.com/cmdcolin/TEnest) (this was an online tool that
does not appear to exist anymore see
https://web.archive.org/web/20170712104431/http://www.plantgdb.org/tool/TEnest/.
the github link is re-hosted source code also downloaded from archive.org)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tenest.jpg)
- [Transposcope](https://github.com/FenyoLab/transposcope)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/transposcope.png)
## Uncategorized
- [Locuszoom.js](http://locuszoom.org/locuszoomjs.php)
## Variation
- [NucFreq](https://github.com/mrvollger/NucFreq)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/nucfreq.png)
- [snpit](https://github.com/aineniamh/snipit)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpit.png)
- [vcfPlotein](https://vcfplotein.liigh.unam.mx/#/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcfplotein.png)
# Other lists
- [Awesome Bioinformatics](https://github.com/danielecook/Awesome-Bioinformatics)
- [Genocat](http://genocat.tools/) large collection of genomic visualizations
with great review paper accompaniment
https://onlinelibrary.wiley.com/doi/full/10.1111/cgf.13727
- [awesome-biological-visualizations](https://github.com/keller-mark/awesome-biological-visualizations)
Send in PRs for more stuff!
## License
This README.md and TOOLS.json are CC0
https://creativecommons.org/publicdomain/zero/1.0/
The website code is MIT