From: JBrowse 2: a modular genome browser with views of synteny and structural variation
Track type | Appears in | Function | Supported file types |
---|---|---|---|
Quantitative Track | Linear Genome View | Displays dense, continuous, quantitative data | BigWig, GC content (from sequence files), GWAS scores (from BED files) |
Synteny Track | Dotplot View, Linear Synteny View | Displays alignments between different genome assemblies | PAF [21],.delta from MUMmer [22], mashmap.out files [23],.chain (UCSC), MCScan.anchors files [24] |
Alignments Track | Linear Genome View | Displays a combination of a pileup and a coverage visualization of alignments | BAM, CRAM |
Hi-C Track | Linear Genome View | Displays Hi-C contact matrix | .hic files, generated by Juicebox [25] |
Variant Track | Linear Genome View, Circular View | Displays feature glyphs corresponding to variants; specialized feature details panel show all genotypes in multi-sample VCF | VCF (plaintext or tabix) |
Feature Track | Linear Genome View | Displays feature glyphs corresponding to genome annotations, e.g. genes | GTF (plaintext), GFF3 (tabix or plaintext), BigBed, BED (tabix or plaintext), features from REST APIs, etc |
Reference Sequence Track | Linear Genome View | Displays a reference/assembly sequence and a three-frame translation | FASTA (indexed FASTA or bgzipped indexed FASTA), TwoBit (.2bit) |