Supported file types

Every track reads data through an adapter whose type selects the reader, and the file's extension picks that type. Find your format in the tables below for the adapter that reads it and a link to its full config docs. Most adapters accept the uri shorthand, and a track over a format listed here can skip both keys — see the whole-track shorthand.

The uri shorthand#

Most adapters accept a uri shorthand: give the data file location and the adapter resolves the companion index by appending the standard suffix (.bai for a .bam, .crai for a .cram, .fai for a .fa, .tbi for a tabix .gz, and so on).

{
  "type": "AlignmentsTrack",
  "trackId": "sample_bam",
  "name": "Sample reads",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BamAdapter",
    "uri": "https://example.com/sample.bam"
  }
}

jbrowse add-track https://example.com/sample.bam \
  --trackId sample_bam \
  --name "Sample reads" \
  --assemblyNames hg38

{
  "type": "AlignmentsTrack",
  "trackId": "sample_bam",
  "name": "Sample reads",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BamAdapter",
    "uri": "https://example.com/sample.bam"
  }
}

• Spell out the slot form (bamLocation plus index.location) only when the index is named differently or lives elsewhere. An adapter that takes an endpoint, a set of files, or another adapter has no shorthand; each adapter's config page states which keys it accepts above its slot table
• Use CSI over TBI/BAI for a chromosome longer than 512 Mb (some plant and animal genomes; CRAM's .crai has no such limit). BAM and the tabix-indexed adapters (VCF, GFF3, BED, BEDGRAPH, MAF, PAF) accept csi: true:

{
  "type": "VariantTrack",
  "trackId": "variants_csi",
  "name": "Variants",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://example.com/variants.vcf.gz",
    "csi": true
  }
}

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "variants_csi",
  "name": "Variants",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://example.com/variants.vcf.gz",
    "csi": true
  }
}'

{
  "type": "VariantTrack",
  "trackId": "variants_csi",
  "name": "Variants",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://example.com/variants.vcf.gz",
    "csi": true
  }
}

The whole-track shorthand#

Every format in the tables below is one JBrowse recognizes by its extension, and that inference runs on a track config too:

{
  "trackId": "sample_bam",
  "uri": "https://example.com/sample.bam",
  "assemblyNames": ["hg38"]
}

jbrowse add-track-json '{
  "trackId": "sample_bam",
  "uri": "https://example.com/sample.bam",
  "assemblyNames": ["hg38"]
}'

{
  "trackId": "sample_bam",
  "uri": "https://example.com/sample.bam",
  "assemblyNames": ["hg38"]
}

The Track type column below names what the track becomes, the Adapter column names what it reads through, name defaults to the file name, and a config declaring exactly one assembly supplies assemblyNames. Write any of those keys yourself to override the guess: an explicit type picks a track type the extension would not, and an adapter block replaces the guessed one outright. A format the tables do not list needs the full form, and so does a file whose extension names one format while it holds another (the shortest track).

Sequence / assembly#

Sequence adapters go in an assembly, not a track.

Most configs name no sequence adapter: give the assembly a name and a sequence-file uri, and JBrowse picks the adapter from the extension and derives the index siblings.

{
  "name": "hg38",
  "uri": "https://example.com/genome.fa"
}

jbrowse add-assembly https://example.com/genome.fa \
  --name hg38

https://example.com/genome.fa
https://example.com/genome.fa.fai

Alignments#

Read alignments are an AlignmentsTrack (alignments track config).

Feature / annotation#

Gene models, repeats, and other interval features are a FeatureTrack. The plain (non-tabix) GFF3, GTF and BED adapters load the whole file into memory, so prefer the tabix or BigBed forms past small files.

GTF gene models#

GTF has no spanning gene line, so the GTF adapters build the gene model themselves: lines sharing a transcript_id group under a transcript, and transcripts sharing a gene_id under a gene. aggregateField names the attribute that labels the gene, and jbrowse sort-gff sorts a GTF for tabix too (quickstart).

Quantitative / signal#

Coverage and other numeric signals are a QuantitativeTrack (quantitative and multi-quantitative track config).

Variants#

VCF and other variant-like data is a VariantTrack (variant track config for SVTYPE coloring and the multi-sample displays).

Synteny / comparative#

Synteny adapters back the dotplot and linear synteny views (synteny track config). Plain PAF loads entirely into memory; jbrowse make-pif converts a large alignment to PIF, which fetches only the alignments in view (large alignments, PIF format).

Multiple alignment (MAF)#

Multiple-species alignments are a MafTrack (MAF track config for the samples array and the zoom-out tier).

Hi-C#

See Hi-C track config. Loop and interaction calls are BEDPE, which loads as a VariantTrack (see Variants).

GWAS / LD#

See GWAS track config.

Text searching#

Text-search adapters power the location search box (text searching).

Inline data#

A FromConfig adapter embeds a small dataset directly in config.json (FromConfig adapters).

Computed from the reference#

Three adapters scan the sequence of whatever assembly the track is displayed against and emit the hits as features, so the track config names neither a file nor a sequence. All three are FeatureTracks, and each adapter page opens with a whole track config:

• MotifListAdapter — a named motif list (restriction enzymes)
• CrisprGuideAdapter — CRISPR guide RNAs
• SequenceSearchAdapter — a single regex

The sequence search guide drives them from the view menu.

See also#

• Configuring tracks
• Configuring assemblies
• Deploying JBrowse Web
• @jbrowse/cli command reference