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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: 3 months 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 (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2024-04-12T22:04:05.000Z (7 months ago)
- Last Synced: 2024-04-14T12:32:06.715Z (7 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 / PowerShell 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 Twitter account here too :) https://twitter.com/awesomegenomev1
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!
## General
- [Genoverse](https://github.com/wtsi-web/Genoverse)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genoverse.png)
- [BasePlayer](https://baseplayer.fi/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/baseplayer.png)
- [Celera genome browser](https://www.csee.umbc.edu/~turner/presentations/bvw2002/sld009.htm)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/celera.jpeg)
- [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)
- [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)
- [Biodalliance](http://www.biodalliance.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/biodalliance.png)
- [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)
- [Gosling](https://gosling.js.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gosling.png)
- [HiGlass](https://higlass.io)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/higlass.png)
- [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)
- [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)
- [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)
- [UTGB (University of Tokyo Genome Browser)](http://utgenome.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/utgb.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)
- [ABrowse (genome browser)](undefined) (Had integrations with BioMart, Taverna)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/abrowse2.png)
- [gtracks](https://gitlab.com/salk-tm/gtracks) (Powered by pyGenomeTracks)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtracks.png)
- [trackplot (python)](https://github.com/ygidtu/trackplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackplot_python.png)
## 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)
- [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)
- [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)
- [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)
- [ERGO](https://www.igenbio.com/ergo)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ergo.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)
- [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)
- [AliView](http://www.ormbunkar.se/aliview/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/aliview.png)
- [BioJS/MSA](https://msa.biojs.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/biojsmsa.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)
- [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)
- [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)
- [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)
- [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)
- [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)
- [seqotron](https://github.com/4ment/seqotron)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqotron.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)
- [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)
- [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)
- [alignfigR](https://cran.r-project.org/web/packages/alignfigR/vignettes/my-vignette.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignfigr.png)
- [alen](https://github.com/jakobnissen/alen)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alen.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)
- [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)
- [AliTreeViz](https://www.npmjs.com/package/alitreeviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alitreeviz.png)
- [ete](http://etetoolkit.org/gallery/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ete.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)
- [seqvisr](https://github.com/vragh/seqvisr/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqvisr.png)
- [Seaview](http://doua.prabi.fr/software/seaview)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seaview.png)
- [CIAlign](undefined) (Has useful utility functions to clean gaps and trim
MSAs)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cialign.png)
- [ggmsa](http://yulab-smu.top/ggmsa/) (See also ggtree)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggmsa.png)
- [CView](https://sourceforge.net/projects/cview/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cview.png)
## Logo
- [LogoJS](https://logojs.wenglab.org/app/gallery/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/logojs.png)
## CNV
- [aCNVViewer](https://github.com/FJD-CEPH/aCNViewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/acnvviewer.png)
- [CNVkit](https://cnvkit.readthedocs.io/en/stable/plots.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvkit.png)
- [BAMScale](https://github.com/ncbi/BAMscale)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamscale.png)
- [cnvCurator](http://www.acsu.buffalo.edu/~lm69/cnvCurator)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvcurator.png)
- [GenomeSpy](https://genomespy.app/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomespy.png)
- [SFARI](https://gene.sfari.org/database/human-gene/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sfari.jpg)
- [SNPitty](https://bitbucket.org/ccbc/snpitty/src/master/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpitty.jpg)
- [GenomePaint](https://genomepaint.stjude.cloud/) (Demos
https://proteinpaint.stjude.org/bam/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomepaint.png)
- [covviz](https://brwnj.github.io/covviz/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/covviz.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 variatnts)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/purple.png)
- [bcftools cnv](https://samtools.github.io/bcftools/howtos/cnv-calling.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bcftools_cnv.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)
- [genevisR](https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genevisr.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)
- [SnoopCGH](http://snoopcgh.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/snoopcgh.jpg)
- [Genovar](http://genovar.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genovar.png)
- [CNANorm](https://www.bioconductor.org/packages/release/bioc/html/CNAnorm.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnanorm.png)
- [Orchestral](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/orchestral.png)
- [CNSpector](https://github.com/PapenfussLab/CNspector)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnspector.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)
- [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)
- [genome_coverage_plotter](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome-coverage-plotter.png)
- [SeeNV](https://github.com/MSBradshaw/SeeNV)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seenv.png)
## Static
- [BAMSnap](https://github.com/parklab/bamsnap)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamsnap.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)
- [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)
- [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)
- [mummer2circos](https://github.com/metagenlab/mummer2circos)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummer2circos.png)
- [cgplot](https://github.com/dfguan/cgplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgplot.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)
- [geneviewer](https://nvelden.github.io/geneviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneviewer.png)
## Gene fusion
- [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)
- [arriba](https://github.com/suhrig/arriba)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/arriba.png)
- [FusionInspector](https://github.com/FusionInspector/FusionInspector/wiki)
(Uses igv.js)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/fusioninspector.png)
- [MAVIS](http://mavis.bcgsc.ca/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mavis.png)
## Alignments viewer
- [GenomeView (java app)](https://genomeview.org/content/quick-start-guide)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeview_java.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)
- [Chromatic](https://chromatic.nci.nih.gov/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromatic.png)
- [Gambit](http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gambit.png)
- [Hawkeye](undefined)
[(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)
- [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)
- [Short read assembly browser](https://rapdb.dna.affrc.go.jp/AssemblyBrowser2/index.html?ref=%22chr01%22&run_id=%22G4toI1%22&start=%22234780%22&end=%22236631%22)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/short_read_assembly_browser.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)
- [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)
- [gw](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gw.png)
- [DrukBam](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/drukbam.png)
- [bamscope](https://github.com/jslfree080/bamscope)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamscope.png)
## Comparative
- [GSSPlayground](https://github.com/orangeSi/GSSplayground)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gssplayground.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)
- [Biodalliance comparative demo](http://biodalliance.org/dev/test-comparative.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/biodalliance_comparative.png)
- [Chromatiblock](https://github.com/mjsull/chromatiblock)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromatiblock.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)
- [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)
- [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)
- [GBrowse_syn](http://gmod.org/wiki/GBrowse_syn)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gbrowse_syn.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)
- [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)
- [GIVE](https://zhong-lab-ucsd.github.io/GIVE_homepage/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/give_hic.png)
- [mauve-viewer](https://github.com/nconrad/mauve-viewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mauve_viewer.png)
- [MCScan (python version)]()
[(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)
- [MizBee](http://www.cs.utah.edu/~miriah/mizbee/Overview.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mizbee.jpg)
- [Multiple genome viewer](http://www.informatics.jax.org/mgv/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mgv.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)
- [progressiveMauve viewer](http://darlinglab.org/mauve/user-guide/viewer.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/progressive_mauve.png)
- [SyMap](http://www.agcol.arizona.edu/software/symap/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/symap.png)
- [Synima](https://github.com/rhysf/Synima)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/synima.png)
- [Synteny browser](https://github.com/TheJacksonLaboratory/syntenybrowser)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jax_synteny_browser.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)
- [Tripal MapViewer](undefined)
[(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)
- [XMatchView](https://www.bcgsc.ca/resources/software/xmatchview)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/xmatchview.png)
- [LinearDisplay.pl](https://github.com/JCVenterInstitute/LinearDisplay) (readme
says to cite this paper)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/lineardisplay.png)
- [FastANI](https://github.com/ParBLiSS/FastANI)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/fastani.jpg)
- [clinker](https://github.com/gamcil/clinker)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/clinker.png)
- [RectChr](https://github.com/BGI-shenzhen/RectChr)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rectchr.png)
- [pretzel](https://github.com/plantinformatics/pretzel)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pretzel.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)
- [WGDI](https://github.com/SunPengChuan/wgdi)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wgdi.png)
- [BRIG](http://brig.sourceforge.net)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/brig.jpg)
- [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)
- [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)
- [syntenyPlotteR](https://github.com/marta-fb/syntenyPlotteR)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntenyplotter.png)
- [chromoMap](https://lakshay-anand.github.io/chromoMap/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromomap.png)
- [SafFire](https://mrvollger.github.io/SafFire/#ref=CHM13_v1.1&query=GRCh38)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/saffire.png)
- [SimpleSynteny](https://www.dveltri.com/simplesynteny/about.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/simplesynteny.jpg)
- [Cinteny](http://cinteny.cchmc.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cinteny.png)
- [AutoGraph](http://autograph.genouest.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/autograph.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)
- [Smash++](https://github.com/smortezah/smashpp)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/smashpp.png)
- [plotsr](https://github.com/schneebergerlab/plotsr) (see also
https://github.com/schneebergerlab/syri)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotsr.png)
- [GenomeMatcher](http://www.ige.tohoku.ac.jp/joho/gmProject/gmmanual.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomematcher.png)
- [SynBrowse](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/synbrowse.png)
- [Sybil](http://sybil.sourceforge.net/) (Download
https://sourceforge.net/projects/sybil/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sybil.png)
- [SyntenyPortal](http://bioinfo.konkuk.ac.kr/synteny_portal/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntenyportal.png)
- [CHROMEISTER](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromeister.png)
- [r2cat](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/r2cat.jpeg)
- [SequenceSurveyor](https://graphics.cs.wisc.edu/Vis/SequenceSurveyor/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequencesurveyor.png)
- [BactoGENIE](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bactogenie.png)
- [PSAT](http://www.nwrce.org/psat)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/psat.png)
- [TreeBrowser (MicrobesOnline)](http://www.microbesonline.org/cgi-bin/treeBrowse.cgi?locus=17761)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/treegenome.png)
- [Combo](undefined) (Based on the tool 'Argo')
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/combo.png)
- [GenomicBreaks](https://oist.github.io/GenomicBreaks/articles/GenomicBreaks.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomicbreaks.png)
- [GenomeSyn](https://github.com/jmsong2/GenomeSyn)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomesyn.png)
- [CrowsNest](https://pgsb.helmholtz-muenchen.de/crowsnest/help.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/crowsnest.png)
- [GGisy](https://github.com/Sanrrone/GGisy)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggisy.png)
- [multiGenomicContext](https://github.com/Sanrrone/multiGenomicContext)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/multicontext.png)
- [AccuSyn](https://accusyn.usask.ca/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/accusyn.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)
- [ShinySyn](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/shinysyn.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)
- [asynt](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/asynt.png)
- [NGenomeSyn](undefined) (See also RectChr)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ngenomesyn.png)
- [chromsyn](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromsyn.png)
- [syntR](https://www.samuklab.com/syntR/articles/syntr_tutorial.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntr.png)
- [GCSnap](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gcsnap.png)
- [ModDotPlot](https://github.com/marbl/ModDotPlot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/moddotplot.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)
- [ntSynt](https://github.com/bcgsc/ntSynt/tree/main/visualization_scripts)
(Uses gggenomes)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ntsynt.png)
- [SYNY](https://github.com/PombertLab/SYNY)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/syny.png)
## Single cell
- [Millefy](https://github.com/yuifu/millefy)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/millefy.png)
- [gingko](http://qb.cshl.edu/ginkgo/?q=/9EiUttUP0CBHs3WnuBa0)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gingko.jpeg)
- [copykat](https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/copykat.png)
- [scCNV_heatmap](https://github.com/StefanKurtenbach/scCNV_heatmap)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sccnv_heatmap.png)
- [casper](https://github.com/akdess/CaSpER)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/casper.png)
- [ArchR](https://www.archrproject.com/articles/Articles/tutorial.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/archr.png)
- [numbat](https://kharchenkolab.github.io/numbat/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/numbat.png)
- [MosaicCatcher pipeline](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mosaicatcher.png)
## GWAS
- [PureScript genetics browser](https://github.com/chfi/purescript-genetics-browser)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/purescript.png)
- [Locuszoom](http://locuszoom.org/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/locuszoom.png)
- [LDBlockShow](https://github.com/BGI-shenzhen/LDBlockShow)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ldblockshow.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)
- [CMPlot](undefined)
[(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)
## Dotplot
- [shinyChromosome](http://150.109.59.144:3838/shinyChromosome/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/shinychromosome.png)
- [D-GENIES](http://dgenies.toulouse.inra.fr/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dgenies.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/)
- [iLambda/Dotplot](https://github.com/iLambda/dotplot)
- [dotPlotly](https://github.com/tpoorten/dotPlotly/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotplotly.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)
- [Jdot](https://github.com/LyonsLab/jdot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jdot.png)
- [last-dotplot](https://gitlab.com/mcfrith/last)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/last_dotplot.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)
- [ggplot2 mummerplot](https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummerplot_ggplot2.png)
- [Redotable](https://github.com/s-andrews/redotable)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/redotable.png)
- [syntenyPlotByR](https://github.com/shingocat/syntenyPlotByR)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/synteny_plot_by_r.png)
- [Dotter](https://sonnhammer.sbc.su.se/Dotter.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotter.png)
- [JGI/IMG](https://img.jgi.doe.gov/) (Dotplot use MUMmer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/jgiimg.png)
- [MashMap](https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/mashmap.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)
- [DAGchainer](http://dagchainer.sourceforge.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/dagchainer.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)
## Gene structure
- [TnT](https://tnt.marlin.pub/articles/introduction)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/tnt.png)
- [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)
## Microbiology
- [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)
- [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)
- [GeneViTo](http://athina.biol.uoa.gr/bioinformatics/GENEVITO/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genevito.jpg)
- [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)
- [clonifier](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/clonifier.png)
## Graph
- [AGB assembly graph browser](undefined)
[(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)
- [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)
- [graphgenomeviewer](https://cmdcolin.github.io/graphgenomeviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/graphgenomeviewer.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)
- [sequence tube map](https://github.com/vgteam/sequenceTubeMap)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequence_tube_map.png)
- [Shasta](https://chanzuckerberg.github.io/shasta/ComputationalMethods.html#ReadGraph)
(Uses graphviz)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/shasta.png)
- [LINX](https://github.com/hartwigmedical/hmftools/blob/master/linx/README.md)
(part of the PURPLE/GRIDSS/LINX pipeline)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/linx.png)
- [GfaViz](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gfaviz.png)
- [panGraphViewer](https://github.com/TF-Chan-Lab/panGraphViewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pangraphviewer.jpg)
- [IGGE](https://github.com/immersivegraphgenomeexplorer/IGGE) (Not open source)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/igge.png)
- [ctag](undefined) (See also hygene
https://github.com/ProgrammingLife2017/hygene)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ctag.png)
- [PGR-TK](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgrtk.png)
- [VRPG](https://github.com/codeatcg/VRPG)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vrpg.png)
- [SGTK (scaffold graph toolkit)](https://olga24912.github.io/SGTK/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sgtk.png)
- [pgv (graph tool)](https://w-gao.github.io/pgv/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgv2.png)
- [VAG](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vag.jpg)
- [waragraph](https://chfi.github.io/waragraph/) (Deployed to the web via wasm)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/waragraph.png)
## SV
- [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)
- [Ribbon](http://genomeribbon.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeribbon.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)
- [SplitThreader](http://splitthreader.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/splitthreader.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)
- [asgart](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/asgart.png)
- [NeoLoopFinder](https://github.com/XiaoTaoWang/NeoLoopFinder)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/neoloopfinder.png)
- [SVPV](https://github.com/VCCRI/SVPV)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svpv.jpg)
- [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)
- [bigly](https://github.com/brentp/bigly)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bigly.png)
- [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)
- [ReConPlot](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/reconplot.png)
- [SVhawkeye](https://github.com/yywan0913/SVhawkeye)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/svhawkeye.jpg)
## 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)
- [plotReads](http://campuspress.yale.edu/knightlab/ruddle/plotreads/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotreads.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)
- [pileuppy](https://gitlab.com/tprodanov/pileuppy)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pileuppy.png)
- [rich-msa](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/richmsa.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)
- [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)
- [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)
- [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)
- [Gview](https://server.gview.ca/examples)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gview.png)
- [RegulomeExplorer](http://explorer.cancerregulome.org/all_pairs/?dataset=TCGA_ACC)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/cancerregulome.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)
- [pyCircos](https://github.com/ponnhide/pyCircos) (See also
https://github.com/ponnhide/plasmidviewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pycircos.png)
- [pyCirclize](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pycirclize.png)
- [OmicCircos](http://bioconductor.org/packages/release/bioc/html/OmicCircos.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/omiccircos.png)
- [genoVi](https://github.com/robotoD/GenoVi)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/genovi.png)
- [BRICK (BRIG-like circular knowledgebase)](https://brick.ink/) (See also BRIG)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/brick.png)
## Synthetic biology
- [seqviz](https://github.com/Lattice-Automation/seqviz#viewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqviz.png)
- [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)
- [plasmapR](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plasmapr.png)
## 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)
- [Internet Contig Explorer](https://www.bcgsc.ca/resources/software/ice)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/internet_contig_explorer.jpg)
## Exotic
- [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)
- [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)
- [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)
## Epigenomics
- [EaSeq](https://easeq.net/screenshots/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/easeq.png)
- [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)
- [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)
- [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)
- [CoolBox](undefined) (fork of pyGenomeTracks)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/coolbox.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)
- [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)
## Linear
- [Gnomad browser](https://github.com/macarthur-lab/gnomadjs)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gnomad.png)
## Expression
- [GTEX Locus browser](https://gtexportal.org/home/locusBrowserPage/ACTN3)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtex_locus.png)
## Population
- [GWAS catalog browser](https://www.ebi.ac.uk/gwas/variants/rs1558902)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gwascatalog.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)
- [PopSV](https://github.com/jmonlong/PopSV/blob/master/3-Visualization.md)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/popsv.png)
- [vcfR](https://knausb.github.io/vcfR_documentation/) (image shows chromoqc
output)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcfr.png)
- [SWAV](http://swav.popgenetics.net/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/swav.png)
- [Haploview](https://www.broadinstitute.org/haploview/haploview)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/haploview.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)
## Assembly QC
- [Icarus QUAST](http://quast.sourceforge.net/icarus.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/icarus.png)
- [ALVIS (chimeric alignment viewer)](https://github.com/SR-Martin/alvis)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/alvis_chimeric.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)
- [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)
## Alignment viewer
- [MagicViewer](http://bioinformatics.zj.cn/magicviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/magicviewer.jpeg)
## Uncategorized
- [Locuszoom.js](http://locuszoom.org/locuszoomjs.php)
## Coverage
- [SeqCover](https://brentp.github.io/seqcover/#gene=AIFM1)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqcover.png)
- [wiggleplotr](http://bioconductor.org/packages/devel/bioc/vignettes/wiggleplotr/inst/doc/wiggleplotr.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wiggleplotr.png)
- [Trackplot (R)](https://github.com/PoisonAlien/trackplot)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackplot.png)
- [signac](https://github.com/timoast/signac/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/signac.png)
- [ggcoverage](https://cran.r-project.org/web/packages/ggcoverage/vignettes/ggcoverage.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggcoverage.png)
- [BAMdash](https://github.com/jonas-fuchs/BAMdash/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamdash.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)
## Pangenome
- [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)
- [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)
- [RPAN (3kricedb)](http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rpan.png)
- [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)
## Transposons
- [TE-nest](undefined) (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](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/transposcope.png)
## Annotation
- [Varsome]()
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/varsome.png)
## Splicing
- [Vials](http://vials.io/)
- [splicejam](https://github.com/jmw86069/splicejam)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/splicejam.png)
- [Slinker](https://github.com/Oshlack/Slinker) (See also, clinker (gene fusion
software))
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/slinker.png)
## Quantitative
- [wasm bigwig demo browser](https://shk656461.github.io/index.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/wasm_bigwig.png)
## Ideogram
- [eweitz/Ideogram](https://github.com/eweitz/ideogram)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/eweitz_ideogram.png)
- [Ideogram](https://github.com/RCollins13/HumanIdiogramLibrary)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/rcollins_ideogram.png)
- [Ideoplot](https://github.com/mchaisso/Ideoplot)
- [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)
- [UCSC Genome Graphs](http://genome.ucsc.edu/cgi-bin/hgGenome)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ucsc_genome_graph.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)
- [IdeoViz](https://www.bioconductor.org/packages/release/bioc/vignettes/IdeoViz/inst/doc/Vignette.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ideoviz.png)
- [Flash Gviewer](http://gmod.org/wiki/Flashgviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/flashgviewer.png)
- [Ideogram viewer](https://bioinformatics.mdanderson.org/public-software/ideogramviewer/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ideogramviewer.png)
- [chromPlot](https://www.bioconductor.org/packages/release/bioc/vignettes/chromPlot/inst/doc/chromPlot.pdf)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromplot.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)
- [ezcharts](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/ezcharts.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)
## Mobile app
- [iGenomics](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/igenomics.png)
## Protein
- [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)
- [Aquaria](http://aquaria.ws/Q9HD67/5i0i/A)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/aquaria.png)
- [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)
- [drawProteins](undefined)
[(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)
- [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)
- [TogoStanza Protein Browser](https://db-dev.jpostdb.org/ts/stanza/protein_browser/help.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/togostanza.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)
## Repeats
- [REPAVER](https://gitlab.com/gringer/bioinfscripts/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/repaver.jpg)
- [GraphAlignmentViewer](https://github.com/Illumina/GraphAlignmentViewer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/graphalignmentviewer.png)
- [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)
- [StainedGlass](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/stainedglass.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)
- [TRVZ (TRGT tandem repeat genotyping visualizer)](https://github.com/PacificBiosciences/trgt)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/trvz.png)
## Methylation
- [NanoMethViz](http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/nanomethviz.png)
- [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)
## Phylogenetics
- [Nextclade](https://clades.nextstrain.org/) (Related usage on nextstrain app
also)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/nextclade.png)
- [Gingr](https://harvest.readthedocs.io/en/latest/content/gingr.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gingr.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)
## Long reads
- [methylartist](https://github.com/adamewing/methylartist)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/methylartist.png)
## Hi-C
- [Plotgardener](https://github.com/PhanstielLab/plotgardener/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotgardener.png)
- [gcMapExplorer](https://github.com/rjdkmr/gcMapExplorer)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gcmapexplorer.png)
- [PretextView](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/pretextview.jpg)
- [figeno](https://github.com/CompEpigen/figeno)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/figeno.png)
## Deadlink
- [VAMP](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/vamp.jpg)
- [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)
## BLAST
- [SequenceServer](https://sequenceserver.com/)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequenceserver.png)
## Academic license
- [Consed](http://bozeman.mbt.washington.edu/consed/consed.html)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/consed.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)
## Variation
- [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)
- [NucFreq](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/nucfreq.png)
## Chromosome painting
- [GeMo](undefined)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/gemo.png)
## K-mer
- [Panagram](https://github.com/kjenike/panagram)
[(img)](https://cmdcolin.github.io/awesome-genome-visualization/panagram.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