awesome-genome-visualization

A list of interesting genome visualizers, genome browsers, or genome-browser-like implementations

Genome browsers

• ATCC Genome Portal
• Ensembl genome browser
• GBrowse
• GBrowse 2
• IGV (java)
• IGV.js
• JBrowse
• NCBI Genome Data Viewer
• Trackster (in Galaxy)
• UCSC genome browser
• WashU epigenomics browser source

Other

• Apollo desktop app. also see WebApollo, built on JBrowse
• 2020 Ensembl genome browser
• Artemis comparison tool (ACT)
• Biodalliance
• BrowseVCF
• CNVnator
• CuteVCF
• DNASkittle
• Epilogos
• GenomeRibbon
• Genoverse
• Gnomad browser
• HiGlass
• IslandPlot (D3, SVG) (source)
• Juicebox
• Locuszoom
• NGB
• Pileup.js
• PureScript genetics browser
• SEQing
• Savant
• SplitThreader
• TASUKE - from RAP-DB
• Tablet
• Valis browser - used on encodeproject.org (uses webGL)
• Varsome
• WebAsm demo browser

Genome map, or comparative viewers

• GBrowseSyn
• SynBrowse
• Aequatus
• Biodalliance comparative demo
• CMap
• CVit
• CrossBrowse
• Cvit.js
• GIVE
• Genome context viewer
• MCScan (python version)
• MCScanX
• Multiple genome viewer
• Synteny browser

Static visualizations

• AliTV
• BAMScale
• BioJS (MSA/msaR)
• CNView
• Chimeraviz
• Circos
• ClustersPloter
• DNAPlotLib
• FeatureViewer
• GGgenes
• Geneviz
• GenomeTools
• GenomeView
• Hagfish
• HiCPlotter
• Methplotlib
• Samplot
• Spliceclust
• genoPlotR
• karyoploteR (R)
• pyGenomeTracks
• svist4get
• svviz2
• svviz
• trackViewer (R)

Dotplot

• D-GENIES
• Dot
• Dotplot
• Jdot
• LAST (package contains a dotplotter)
• Minidot
• Mummer (contains a GNUplot script for dotplotting)
• Redottable

Karyotype

• Ideogram HumanIdeogramLibrary
• Ideogram (SVG)
• Karyotype
• RNA-seq view

Command line

• ASCIIGenome
• Alan
• Alv
• Bamcov
• Hapviz
• Sam2pairwise
• Samtools tview

Graph genomes

• Bandage
• gGnomes.js
• sequence tube map

Other lists

• Awesome Bioinformatics

Send in PRs for more stuff!