awesome-genome-visualization
A list of interesting genome browser and genome visualization programs
https://github.com/cmdcolin/awesome-genome-visualization
Last synced: 9 days ago
JSON representation
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Academic license
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Alignments
- GenomeView (java app) - genome-visualization/genomeview_java.png)
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- Chromatic - genome-visualization/chromatic.png)
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- Gambit - genome-visualization/gambit.png)
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- LookSeq - genome-visualization/lookseq.png)
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- Staden - genome-visualization/staden.png)
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- alignoth - genome-visualization/alignoth.png)
- bamscope - genome-visualization/bamscope.png)
- DrukBam - genome-visualization/drukbam.png)
- gw - genome-visualization/gw.png)
- Hawkeye - genome-visualization/hawkeye.png)
- MagicViewer - genome-visualization/magicviewer.jpeg)
- NGB - genome-visualization/ngb.png)
- pyBamView - genome-visualization/pybamview.png)
- udon - genome-visualization/udon.png)
- wally - genome-visualization/wally.png)
- MapView - genome-visualization/mapview.jpg)
- MapView - genome-visualization/mapview.jpg)
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Alignments viewer
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Annotation
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Assembly
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Assembly QC
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- vega
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- ALVIS (chimeric alignment viewer) - genome-visualization/alvis_chimeric.png)
- Consed - genome-visualization/consed.png)
- vega - genome-visualization/vega.png)
- Icarus QUAST - genome-visualization/icarus.png)
- MIRA - genome-visualization/mira.png)
- Genome Puzzle Master (GPM) - genome-visualization/gpm.png)
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based
- Rna Alignment Viewers (Colorstock, SScolor, Ratón) - genome-visualization/rnaalignment.png)
- Alan - genome-visualization/alan.png)
- Alv - genome-visualization/alv.png)
- ASCIIGenome - genome-visualization/asciigenome.png)
- Bamcov - genome-visualization/bamcov.png)
- Hapviz - genome-visualization/hapviz.png)
- pileuppy - genome-visualization/pileuppy.png)
- rich-msa - genome-visualization/richmsa.png)
- Sam2pairwise
- Samtools tview - genome-visualization/tview.png)
- SeqSizzle - genome-visualization/seqsizzle.png)
- SvABA - genome-visualization/svaba.png)
- VizAln (from HipSTR) - genome-visualization/hipstr.png)
- wgatools - genome-visualization/wgatools.png)
- plotReads - genome-visualization/plotreads.png)
- Samtools depth visualization - genome-visualization/depthplot.png)
- tgv (terminal genome viewer) - genome-visualization/tgv.png)
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BLAST
- SequenceServer - genome-visualization/sequenceserver.png)
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Chromosome painting
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Circular
- Anvio
- BioCircos.js
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- Circleator
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- Circos - genome-visualization/circos.png)
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- GenomeProjector - genome-visualization/glanguage.jpg)
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- OGDRAW - genome-visualization/ogdraw.png)
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- Gview
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- RegulomeExplorer
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- OmicCircos - genome-visualization/omiccircos.png)
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- BRICK (BRIG-like circular knowledgebase) - genome-visualization/brick.png)
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- RegulomeExplorer - genome-visualization/cancerregulome.png)
- BioCircos.js - genome-visualization/biocircos.png)
- Circleator - genome-visualization/circleator.png)
- circlize - genome-visualization/circlize.jpeg)
- CircosJS - genome-visualization/circosjs.png)
- circularMT - genome-visualization/circularmt.png)
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- genoVi - genome-visualization/genovi.png)
- Gview - genome-visualization/gview.png)
- JupiterPlot - genome-visualization/jupiterplot.png)
- pyCirclize - genome-visualization/pycirclize.png)
- pyCircos - genome-visualization/pycircos.png)
- CGView - genome-visualization/cgview.png)
- CGView.js - genome-visualization/cgviewjs.png)
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- DNAPlotter - genome-visualization/dnaplotter.jpg)
- OmicCircos - genome-visualization/omiccircos.png)
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CNV
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- CNVkit - genome-visualization/cnvkit.png)
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- GenomeSpy - genome-visualization/genomespy.png)
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- GenomePaint
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- bcftools cnv - genome-visualization/bcftools_cnv.png)
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- genevisR - genome-visualization/genevisr.png)
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- SnoopCGH
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- Genovar
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- CNANorm - genome-visualization/cnanorm.png)
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- SFARI - genome-visualization/sfari.jpg)
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- CoveragePlotter
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- aCNVViewer - genome-visualization/acnvviewer.png)
- BAMScale - genome-visualization/bamscale.png)
- CNSpector - genome-visualization/cnspector.png)
- CoveragePlotter - chromosome) [(img)](https://cmdcolin.github.io/awesome-genome-visualization/coverageplotter.png)
- covviz - genome-visualization/covviz.png)
- genome_coverage_plotter - genome-visualization/genome-coverage-plotter.png)
- mocha - genome-visualization/mocha.png)
- SeeNV - genome-visualization/seenv.png)
- Genovar - genome-visualization/genovar.png)
- SnoopCGH - genome-visualization/snoopcgh.jpg)
- GenomePaint - genome-visualization/genomepaint.png)
- cnvCurator - genome-visualization/cnvcurator.png)
- copynumber - genome-visualization/copynumber.png)
- PURPLE - 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)
- sequenza - genome-visualization/sequenza.png)
- SNPitty - genome-visualization/snpitty.jpg)
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Commercial
- 10x genomics - Loupe - genome-visualization/10xgenomics.png)
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- Alamut
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- ATCC Genome Portal - genome-visualization/atcc.png)
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- Benchling - genome-visualization/benchling.png)
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- CLC Genomics workbench - genome-visualization/clcgenomics.png)
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- DNASTAR - genome-visualization/dnastar.png)
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- Geneious - genome-visualization/geneious.png)
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- Golden Helix - genome-visualization/goldenhelix.png)
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- MacVector - genome-visualization/macvector.png)
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- Persephone - genome-visualization/persephone.jpg)
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- SnapGene - genome-visualization/snapgene.png)
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- Strand NGS - genome-visualization/strandngs.png)
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- Bionano
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Programming Languages
Categories
Comparative
210
Static
136
MSA
95
General
73
Dotplot
53
CNV
49
Circular
44
Graph
43
Commercial
39
SV
37
Ideogram
34
Alignments
33
Epigenomics
28
Protein
26
Pangenome
21
Population
18
Text based
18
Single cell
18
based
17
Gene fusion
16
Coverage
15
Microbiology
15
GWAS
14
Assembly QC
13
Repeats
13
Exotic
13
Hi-C
10
Synthetic biology
10
Gene structure
9
Variation
9
Alignments viewer
8
Multi-way synteny
8
Phylogenetics
8
Splicing
7
Special-purpose
7
Historical
7
Local ancestry
7
Methylation
6
Uncategorized
5
Manhattan
4
Heatmap
4
Transposons
4
Deadlink
3
K-mer
3
Linear
2
Mobile app
2
Long reads
2
BLAST
2
Assembly
2
Logo
2
Expression
2
Chromosome painting
2
Quantitative
2
Annotation
1
Academic license
1
Sub Categories
Keywords
bioinformatics
16
visualization
15
genomics
10
data-visualization
6
genomics-visualization
6
comparative-genomics
5
python
5
genome
5
r
4
phylogenetic-trees
3
matplotlib
3
circos
3
microbial-genomics
3
bam
3
javascript
3
genbank
2
vcf
2
sequence-alignment
2
alignment
2
big-data
2
c-plus-plus
2
ggplot2
2
synteny
2
genetics
2
genome-viewer
2
d3js
2
awesome
2
awesome-list
2
tui
2
rust
2
msa
2
hpc
2
biology
2
cancer
2
transcriptomics
2
cancer-genomics
2
visualisation
2
biopython
2
pangenome
2
synthetic-biology
2
assembly
1
contigs
1
graph-genome-browser
1
structural-variants
1
mapping
1
variation-graph
1
vizualisation
1
plotting
1
sequencing
1
sequencing-data
1