awesome-genome-visualization

A list of interesting genome browser and genome visualization programs
https://github.com/cmdcolin/awesome-genome-visualization

Last synced: 18 days ago
JSON representation

Static
- svist4get
- svist4get
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- Genome STRiP
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- GenomeTools
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- ggbio
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- gtrellis
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- Gviz
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- Hagfish
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- Mason
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- Pairoscope
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- pauvre
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- RACER
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- svist4get
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- trackViewer
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- svist4get
- svist4get - genome-visualization/svis4get.png)
- svist4get
- svist4get
- svist4get - genome-visualization/svis4get.png)
- Geneviz
- genoPlotR
- JVarKit/BamToSVG
- RepViz
- SashimiPlot
- Sushi
- svist4get - genome-visualization/svis4get.png)
- bcftools roh
- svist4get - genome-visualization/svis4get.png)
- svist4get
- svist4get - genome-visualization/svis4get.png)
- svist4get - genome-visualization/svis4get.png)
- svist4get
- svist4get
- svist4get
- ExonIntron
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
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- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
- svist4get
General
- Genoverse
- IGV.js
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- BasePlayer
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- IGB
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- Ensembl genome browser
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- Ensembl genome browser 2020 edition
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- GBrowse 2
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- GenomeMaps
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- Gosling
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- HiGlass
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- JBrowse
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- JBrowse 2
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- Kero-BROWSE
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- Nucleome browser
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- Zenbu
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- UTGB (University of Tokyo Genome Browser)
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- Argo
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- IGV
- Savant
- Tablet
- Biodalliance
- Ensembl genome browser
- Trackster
- UCSC genome browser
- Valis browser
- WashU epigenomics browser
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- NCBI Genome Data Viewer
- Celera genome browser
Commercial
- 10x genomics/Loupe
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- Alamut
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- Golden Helix
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- MacVector
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- Persephone
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- SnapGene
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- Strand NGS
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- Bionano
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- ERGO
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- ATCC Genome Portal
- Benchling
- CLC Genomics workbench
- DNASTAR
- Geneious
- Genestack
- Circa
MSA
- AA (alignment annotator)
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- rMSA
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- Boxshade
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- ESPript
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- Jalview
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- JSAV
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- SNIPViz
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- ALVIS (MSA viewer)
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- alignfigR
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- ProViz
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- MEGA-X
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- AliTreeViz
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- ete
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- Seaview
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- ggmsa
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- CView
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- AlignmentComparator
- AlignmentViewer
- AliView
- BioJS/MSA
- MSABrowser
- MView
- NCBI MSA Viewer
- STRAP
- TeXShade
- Wasabi
Logo
- LogoJS
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CNV
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- CNVkit
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- GenomePaint
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- PURPLE
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- bcftools cnv
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- SnoopCGH
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- Genovar
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- CNANorm
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- cnvCurator
- GenomeSpy
- genevisR
- copynumber
- CoveragePlotter
- SFARI
- sequenza
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Gene fusion
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- FusionInspector
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- MAVIS
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Comparative
- PSAT
- PSAT - genome-visualization/psat.png)
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- AliTV
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- Biodalliance comparative demo
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- CoGe
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- MizBee
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- XMatchView
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- PipMaker
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- miropeats
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- chromoMap
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- SyntenyPortal
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- SequenceSurveyor
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- PSAT
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- TreeBrowser (MicrobesOnline)
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- PSAT - genome-visualization/psat.png)
- CMap
- Comparative assembly hub / "snake track"
- CVit
- GBrowse_syn
- Genome Context Viewer
- Genomicus
- SynTView
- SynVisio
- SimpleSynteny
- Cinteny
- AutoGraph
- EvolutionHighway
- PSAT - genome-visualization/psat.png)
- CrowsNest
- AccuSyn
- NCBI CGV
- syntR
- PSAT - genome-visualization/psat.png)
- PSAT - genome-visualization/psat.png)
- PSAT - genome-visualization/psat.png)
- PSAT
- Multiple genome viewer
- OMA local synteny browser
- Parasight
- SyMap
- PSAT
- GenomicBreaks
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- PSAT
- PSAT
- GenomeMatcher
- PSAT
- ntSynt
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- PSAT
- PSAT
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- PSAT
Single cell
- gingko
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- copykat
- ArchR
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Ideogram
- UCSC Genome Graphs
- IdeoViz
- Flash Gviewer
- Ideogram viewer
- chromPlot
- PhenoGram
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Protein
- ProteinPaint
- Aquaria
- IBS (Illustrator for Biological Sequences)
- PFAM generate_graphic
- Prosite/MyDomains
- TogoStanza Protein Browser
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Pangenome
- Pan-Tetris
- PGAP-X
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- TASUKE - genome-browser
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Heatmap
- UCSC Xena
- VIVA
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Repeats
- SODA - level library to
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- REPAVER
Historical
- Internet Contig Explorer
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- Apollo
Methylation
- AnnoJ
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Phylogenetics
- Nextclade
- Gingr
- Taxonium - genome-visualization/taxonium.png)
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Assembly QC
- vega
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Coverage
- ggcoverage
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BLAST
- SequenceServer
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Academic license
- Consed
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Local ancestry
- fineSTRUCTURE aka ChromoPainter
- MOSAIC
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Variation
- vcfPlotein
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K-mer
- Awesome Bioinformatics
- Genocat
- awesome-biological-visualizations
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Alignments viewer
- GenomeView (java app)
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- Chromatic
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- MapView
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- alignoth - genome-visualization/alignoth.png)
- Short read assembly browser
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- Gambit
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- LookSeq
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- Staden
GWAS
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- Locuszoom
- ggplot2 manhattan plot
Dotplot
- shinyChromosome
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- Dotplot (chirimoyo)
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- Dottup
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- ggplot2 mummerplot
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- Dotter
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- Dot
- Dotlet
- JGI/IMG
- MashMap
- Gepard
Gene structure
- TnT
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- Apollo aka WebApollo
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- D3GB
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Microbiology
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- GeneViTo
- GECO
- GeCoViz
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Graph
- AGB assembly graph browser
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- odgi draw + odgi viz + odgi inject
- Shasta
- LINX
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SV
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- Gremlin
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- Introgression browser
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- SMRT View
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- SVhawkeye
- Ribbon
Text based
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- Rna Alignment Viewers (Colorstock, SScolor, Ratón)
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- Samtools depth visualization
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- Samtools tview
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Circular
- Anvio
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- Circos
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- OmicCircos - genome-visualization/omiccircos.png)
- BioCircos.js
- Circleator
- GenomeProjector
- OGDRAW
- Gview
- RegulomeExplorer
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- BRICK (BRIG-like circular knowledgebase)
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- RegulomeExplorer
Synthetic biology
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- ApE (a plasmid editor)
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- Chopchop
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Special-purpose
- Apollo
- Panoptes
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- UGENE
Exotic
- DNASkittle
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- FluentDNA
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- Cylindrical alignment app
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- sockeye
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Epigenomics
- EaSeq
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- JBR - genome-visualization/jbr.png)
- python-genome-browser aka pygbrowse
- Chip Monk
- Chipster
- cisGenome Browser
- Epilogos
- Epiviz
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Linear
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Alignment viewer
- MagicViewer
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Population
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- PopSV
- SWAV
- Haploview
- pixy
- GWAS catalog browser
- Human genome dating
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- Panoptes
Transposons
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Annotation
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Splicing
- Vials
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Quantitative
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- wasm bigwig demo browser
Expression
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- GTEX Locus browser
Mobile app
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Long reads
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Hi-C
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Deadlink
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Chromosome painting
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Uncategorized
- Locuszoom.js

Programming Languages

Python 1 HTML 1 JavaScript 1

Categories

Comparative 135 Static 98 MSA 64 General 59 CNV 37 Dotplot 34 Commercial 33 Circular 28 Alignments viewer 24 Graph 23 Ideogram 22 Epigenomics 21 SV 21 Text based 16 Protein 16 Population 15 Pangenome 13 Single cell 11 Exotic 10 Microbiology 9 Repeats 8 GWAS 8 Gene fusion 7 Gene structure 7 Coverage 7 Synthetic biology 6 Phylogenetics 6 Special-purpose 5 Assembly QC 5 Local ancestry 4 K-mer 4 Methylation 4 Heatmap 4 Variation 4 Hi-C 4 Historical 4 Splicing 3 Deadlink 3 Transposons 2 Alignment viewer 2 BLAST 2 Logo 2 Expression 2 Academic license 2 Quantitative 2 Uncategorized 1 Linear 1 Mobile app 1 Long reads 1 Annotation 1 Chromosome painting 1

Sub Categories

Keywords

awesome-list 2 awesome 2 visualization 1 transcriptomics 1 medicine 1 genomics 1 data-visualization 1 cancer 1 biology 1 bioinformatics 1 visualisation 1 genome 1