A list of interesting genome visualizers, genome browsers, or genome-browser-like implementations
Update: I have started to convert this into a CSV format for more rich
metadata. See TOOLS.csv. The formatting on this is not perfect and
if you are reading into R use read.table('TOOLS.csv', fill=T). PRs
contributing to the formatting, or additional richness of this metadata are
welcome! I still like the "awesome-list" format but it is not structured enough
to contain extra columns of data, etc. Possibly the awesome-list will be
generated by the CSV in the future
- BasePlayer
- IGB
- IGV (java)
- Savant
- Tablet
- Biodalliance
- Ensembl genome browser
- Ensembl genome browser 2020 edition
- GBrowse+GBrowse 2
- GenomeMaps (used on ICGC)
- HiGlass (has epigenomics focus but quite advanced)
- IGV.js
- JBrowse [can run on desktop via Electron]
- JBrowse 2 (under development)
- NCBI Genome Data Viewer
- Pileup.js
- UCSC genome browser
- Trackster (in Galaxy)
- WashU epigenomics browser source
- Valis browser - used on encodeproject.org (uses webGL)
- Zenbu
- 10x genomics
- Alamut
- Benchling
- ATCC Genome Portal
- CLC Genomics workbench
- DNASTAR
- Geneious
- Genestack
- Golden Helix
- Lucid viewer
- MacVector
- Persephone
- SnapGene
- Strand NGS
- Chip Monk
- Chipster
- cisGenome Browser
- Epilogos
- Epiviz
- HiGlass (has epigenomics focus but quite advanced)
- HiC browser - UCSC-based
- Juicebox and Juicebox.js
- ApE (a plasmid editor)
- Apollo (old desktop version)
- Apollo aka WebApollo
- Chromatic (pub https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987889/)
- cnvCurator
- CNVnator
- DNASkittle also see FluentDNA
- EaSeq
- Gambit
- GenomeRibbon
- GenomeSpy another demo
- Genoverse
- Gnomad browser
- Gremlin
- GTEX Locus browser
- GWAS catalog browser at EBI
- Hawkeye
- Human genome dating (made with vega/d3)
- Icarus
- Introgression browser
- InGAP-SV
- IslandPlot (D3, SVG) (source)
- Locuszoom
- LookSeq (screenshot) (github)
- MagicViewer
- MalariaGEN
- MapView (note: links in original paper are dead. download link here https://sites.google.com/site/wjwdavy/)
- NGB
- Panoptes see malariagen browser
- Parasight
- RNASeqBrowser UCSC-based
- SEQing
- SFARI
- SNPViz
- SNPitty (pub https://jmd.amjpathol.org/article/S1525-1578(17)30166-6/fulltext)
- Staden
- SplitThreader also see GenomeRibbon
- TASUKE - from RAP-DB
- UGENE
- Varsome
- Vials
- wasm bigwig demo browser
- Aequatus
- AliTV
- Artemis comparison tool (ACT)
- Biodalliance comparative demo
- Chromatiblock
- CMap
- CoGe
- Comparative assembly hub / "snake track" (UCSC based)
- CVit
- Cvit.js
- CrossBrowse pub
- EasyFig
- Edinburgh-Genome-Foundry/DnaFeaturesViewer
- Genomicus
- genoplotR
- gggenomes
- Genome Context Viewer (blog post)
- GIVE
- GBrowse_syn
- mauve-viewer
- MCScan (python version)
- MCScanX
- MizBee
- Multiple genome viewer (jax)
- mGSV
- OMA local synteny browser
- pafr
- plotsr from SyRI
- progressiveMauve viewer
- Synteny browser (jax)
- SynTView (webpage)
- SyMap
- Synima
- SynVisio
- VISTA browser
- XMatchView
- AA also see Java web applet version STRAP
- abrowse
- AlignmentViewer
- AliView
- BioJS/MSA also see msa/R
- Boxshade
- ESPript
- Jalview
- JSAV link
- LogoJS
- MView
- React MSAViewer
- seqotron
- TeXShade
- Wasabi
- aCNVViewer (github)
- BAMScale
- ChIA-Pipe
- Chimeraviz
- ClustersPloter
- CNView
- CNVpytor
- CNVPlot
- DNAPlotLib
- ExonIntron from WormBase
- FeatureViewer
- ggbio
- GGgenes
- GGsashimi
- gtrellis
- genoPlotR
- Geneviz
- Genome STRiP
- GenomeTools
- GenomeView
- GSDraw
- Gviz
- Hagfish
- HiCPlotter
- JVarKit examples http://lindenb.github.io/jvarkit/BamToSVG.html
- Lollipops
- Mason
- Millefy single cell
- Pairoscope
- pauvre (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991124/figure/fig-3/ for example)
- PureScript genetics browser
- Methplotlib
- RACER
- RepViz
- Samplot
- SashimiPlot
- shebam
- shinyChromosome
- SNPduo
- SparK
- Spliceclust
- Sushi (R package)
- pyGenomeTracks
- svist4get
- svviz2
- svviz
- svv (stupid simple structural variant view)
- TnT
- trackViewer (R)
- Anvio
- BioCircos.js
- Circos
- CircosJS
- Circleator
- circlize
- DNAPlotter
- GenomeProjector [multiple uses, not just circular]
- JupiterPlot
- mummer2circos
- OGDRAW
- cgplot
- D-GENIES
- Delly-maze
- Discoplot
- Dot
- Dotplot (iLambda)
- Dotplot (chirimoyo)
- dotPlotly
- Gepard
- Jdot
- LAST (package contains a dotplotter)
- mcutils source
- Minidot
- Mummer (contains a GNUplot script, mummerplot, for dotplotting)
- Redottable
- syntenyPlotByR
- chromoMap
- Ideogram HumanIdeogramLibrary
- NCBI Genome Decoration
- eweitz/Ideogram
- KaryotypeSVG
- rnaseqview
- karyoploteR (R package)
- UCSC Genome Graphs
- Ideoplot
- ASCIIGenome
- Alan
- Alv
- Bamcov
- bioSyntax
- BLAST+ <-- reading -outfmt 0 pairwise output is essentially a textual/command line bioinformatics tool
- Hapviz
- plotReads [includes static graphic and text visualization]
- pyBamView
- Rna Alignment Viewers ref https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109877/
- Sam2pairwise
- Samtools tview (keyboard shortcuts)
- VizAln from HipSTR
- Samtools depth visualization
- AGB assembly graph browser
- Bandage
- gGnomes.js
- MoMi-G
- sequence tube map
- graphgenomeviewer (note: I made this during bcc2020 hackathon)
- odgi (ref https://pangenome.github.io/odgi/odgi_docs.html#_odgi_viz1)
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/
- RPAN http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF
- panX http://pangenome.tuebingen.mpg.de/
- Panache https://github.com/SingingMeerkat/Panache
- Awesome Bioinformatics
- Genocat large collection of genomic visualizations with great review paper accompaniment https://onlinelibrary.wiley.com/doi/full/10.1111/cgf.13727
- awesome-biological-visualizations
Send in PRs for more stuff!
This README.md and TOOLS.csv are CC0 https://creativecommons.org/publicdomain/zero/1.0/