Table 2 The list of available track types in JBrowse 2, which are specialized to render different kinds of data from various sources or file formats. Some of the tracks can be used in multiple view types as well
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) |