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Configuration schema

Auto-generated reference for every configuration type: the slots available on each adapter, track, display, and other config object. These pages are generated from the configSchema definitions in the source, so they always match the current release.

For what the format is and where it is accepted, see Config and session JSON; for how configuration fits together, start with the config guide. For the file formats each adapter reads, see supported file types.

Adapter

  • BamAdapter — Reads BAM alignment files, with a BAI or CSI index.
  • BamIndex — Where a BAM's index is and which of the two kinds it is. indexType is derived from the index file's own name where the config names a .csi and leaves it unset, so the usual config states neither —…
  • BedAdapter — Reads plain-text BED files. The adapter loads the whole file into memory, so use BedTabixAdapter for large files.
  • BedGraphAdapter — Reads plain-text bedGraph signal files. The adapter loads the whole file into memory, so use BedGraphTabixAdapter for large files.
  • BedGraphTabixAdapter — Reads bgzip-compressed, tabix-indexed bedGraph signal files.
  • BedpeAdapter — Reads BEDPE files of paired breakends, such as structural variant calls within a single assembly.
  • BedTabixAdapter — Reads bgzip-compressed, tabix-indexed BED files.
  • BgzipFastaAdapter — Reads a bgzip-compressed FASTA reference sequence, with its .fai and .gzi indexes.
  • BgzipMafAdapter — A bgzip-compressed MAF with a Taffy .tai index — the form whole-genome multiple alignments are actually distributed in.
  • BgzipTaffyAdapter — Reads a bgzip-compressed TAF (Taffy) multiple alignment file through its .tai index.
  • BigBedAdapter — Reads BigBed files, the indexed binary form of BED.
  • BigBedTextSearchAdapter — Finds features by the names a BigBed was built to look up, its bedToBigBed -extraIndex columns, which a UCSC hub declares with searchIndex.
  • BigMafAdapter — Reads a UCSC bigMaf file, a BigBed that holds a MAF multiple alignment block in each record.
  • BigWigAdapter — Reads BigWig quantitative signal files.
  • BlastTabularAdapter — Reads BLAST tabular output (-outfmt 6 or 7) as pairwise alignments between a query and a target assembly.
  • ChainAdapter — Reads UCSC chain alignment files, which need the query and target assembly names.
  • ChromSizesAdapter — Reads the chromosome names and lengths in a UCSC-style .chrom.sizes file (tab-separated name<TAB>length), for an assembly with no sequence.
  • CramAdapter — Reads CRAM alignments, fetching only the containers overlapping the visible region through the .crai index.
  • CrisprGuideAdapter — Note: don't set sequenceAdapter — JBrowse supplies it from the assembly the track is displayed against.
  • CytobandAdapter — Reads an assembly's cytoband file, which the linear genome view draws as ideogram banding in its overview bar.
  • DeltaAdapter — Reads MUMmer .delta alignment files, which need the query and target assembly names.
  • FromConfigAdapter — Supplies features written inline in the config, for a small feature set added through a URL or session spec.
  • FromConfigRegionsAdapter — Supplies an assembly's reference names and sizes inline in the config, with no sequence.
  • FromConfigSequenceAdapter — Supplies a reference sequence inline in the config, as features whose seq holds the bases for each region.
  • GCContentAdapter — Computes GC content (or GC skew) from an assembly's sequence at render time, so there is no data file to prepare: the sequence comes from the assembly the track is displayed against.
  • Gff3Adapter — Reads plain-text GFF3 files. The adapter loads the whole file into memory, so use Gff3TabixAdapter for large files.
  • Gff3TabixAdapter — Reads bgzip-compressed, tabix-indexed GFF3 files.
  • GtfAdapter — Reads plain-text GTF files, optionally gzipped. The adapter loads the whole file into memory, so use GtfTabixAdapter for large files.
  • GtfTabixAdapter — Reads bgzip-compressed, tabix-indexed GTF files.
  • GWASAdapter — Reads GWAS results from a bgzip-compressed, tabix-indexed BED-like file.
  • HicAdapter — Reads Hi-C contact matrices from a .hic file.
  • HtsgetBamAdapter — Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam library
  • IndexedFastaAdapter — Reads an uncompressed FASTA reference sequence through its samtools faidx index, fetching the bases in view as byte ranges.
  • JBrowse1TextSearchAdapter — Searches a names index written by JBrowse 1's generate-names.pl. The tracks and assemblyNames slots list the tracks and assemblies the index covers.
  • MafTabixAdapter — Multiple alignment format converted to a bgzipped, tabix-indexed BED.
  • MashMapAdapter — Reads MashMap .out alignment files, which need the query and target assembly names.
  • MCScanAnchorsAdapter — Reads gene-level synteny from an MCScan (jcvi) .anchors file and the two BED files that place its genes.
  • MCScanBlocksAdapter — Loads a multi-genome MCScan (jcvi) .blocks file: a reference-anchored, tab-delimited table where column 0 is a reference gene and each further column is that gene's ortholog in another genome (. = no…
  • MCScanSimpleAnchorsAdapter — Reads synteny blocks from an MCScan (jcvi) .anchors.simple file and the two BED files that place its genes.
  • MotifListAdapter — Scans the reference for a list of named motifs, e.g. restriction enzyme recognition sites.
  • MultiGenomeIndexedPAFAdapter — The tabix-indexed (PIF) form of the MultiGenomePAFAdapter.
  • MultiGenomePAFAdapter — Loads a single PAF holding alignments among several genomes, where every sequence name is PanSN-prefixed with its assembly (sample#haplotype#contig).
  • MultiPairwiseSyntenyAdapter — Composes pairwise synteny adapters that all name one assembly — the anchor — into the star an N-genome view draws from one track: hg38 against each UCSC genome's liftOver PIF, say.
  • MultiWiggleAdapter — Reads several BigWig files as the sources of one multi-row quantitative track.
  • NcbiSequenceReportAliasAdapter — Reads refName aliases for an assembly from an NCBI sequencereport.tsv file.
  • NCListAdapter — Reads a JBrowse 1 NCList feature store, the per-reference trackData.json files that the JBrowse 1 formatting scripts write.
  • PAFAdapter — Reads PAF pairwise alignment files, as written by minimap2 or wfmash, into memory.
  • PairwiseIndexedPAFAdapter — Reads a tabix-indexed PAF (PIF) file, fetching only the alignments in view, for large synteny datasets. The uri shorthand auto-resolves the .tbi index (pass csi: true for a .csi index).
  • PlinkLDAdapter — Adapter for reading pre-computed LD data from a PLINK LD table, either PLINK 2.0's .vcor or PLINK 1.9's .ld. Loads the entire file into memory - suitable for small to medium files.
  • PlinkLDTabixAdapter — Adapter for reading pre-computed LD data from a PLINK LD table (tabix-indexed), either PLINK 2.0's .vcor or PLINK 1.9's .ld.
  • RefNameAliasAdapter — Reads refName aliases for an assembly from a UCSC chromAlias file or any other tab-separated table of aliases.
  • SamAdapter — Reads plain-text SAM alignments, from a file or an inline string.
  • SequenceSearchAdapter — Note: don't set sequenceAdapter — JBrowse supplies it from the assembly the track is displayed against.
  • SPARQLAdapter — Fetches features from a SPARQL endpoint, substituting the queried region into a query template.
  • SplitVcfTabixAdapter — Reads a set of tabix-indexed VCF files, one per chromosome and keyed by refName, for a large call set split by chromosome.
  • StarFusionAdapter — Reads the gene fusions that STAR-Fusion predicts, from its star-fusion.fusionpredictions.tsv output.
  • TabixIndex — The index every tabix-indexed adapter hangs off itself: where the index is, and which of the two kinds it is. indexType is derived from the index file's own name where the config names a .csi and…
  • TrixTextSearchAdapter — Looks up search-box terms in a Trix index (.ix and .ixx) built by jbrowse text-index.
  • TwoBitAdapter — Reads a UCSC .2bit reference sequence, optionally with a chrom.sizes file to speed up loading.
  • UnindexedFastaAdapter — Reads a plain (non-bgzipped) FASTA file with no index. The adapter holds the whole sequence in memory, so use IndexedFastaAdapter for large genomes.
  • VcfAdapter — Reads plain-text (non-bgzipped) VCF files. The adapter loads the whole file into memory, so use VcfTabixAdapter for large files.
  • VcfTabixAdapter — Reads bgzip-compressed, tabix-indexed VCF files.

Assembly Management

  • BaseAssembly — This corresponds to the assemblies section of the config

Connection

  • BaseConnection — Holds a connection's name and the assemblies its tracks belong to. Every connection type has these slots.
  • JB2TrackHubConnection — Adds the tracks of another JBrowse 2 config.json to the session, along with any assemblies it declares that the session lacks.
  • JBrowse1Connection — Adds the tracks of a JBrowse 1 data directory to the session, translated to their JBrowse 2 equivalents.
  • UCSCTrackHubConnection — Adds the tracks a UCSC track hub's hub.txt declares for each matching assembly to the session.

Display

  • AlignmentsArcColor — The alignments displays' arcColor setting colors the read-connection arcs and the read cloud.
  • AlignmentsBaseColor — The alignments displays' baseColor setting: the per-base variable painted as a cell per base over the reads, whatever color fills them with. modifications paints the MM/ML calls and bisulfite the…
  • AlignmentsColor — The alignments displays' color setting: one color for every read, or a field each read carries.
  • AlignmentsModifications — The alignments displays' modifications setting configures the modifications and bisulfite fields of AlignmentsBaseColor.
  • AlignmentsSort — The alignments displays' sort setting: the pileup's row order.
  • BaseLinearDisplay — Shared base config for linear displays — its slots (height, fetchSizeLimit) are common to all of them.
  • ChordColor — A variant chord's color: a CSS color or jexl: callback in value for every chord, or a field of the record whose values each take a range color, with a key on the circle. svType paints the…
  • ChordSyntenyDisplay — Draws a SyntenyTrack in a CircularView, with a ribbon joining the two spans of each alignment.
  • ChordVariantDisplay — Draws the structural variants of a VariantTrack in a CircularView, each translocation as a chord across the circle.
  • DotplotDisplay — Draws a SyntenyTrack as a dot plot inside a DotplotView.
  • Facet — The facet setting of the feature, multi-sample variant, multi-row and alignments displays: one labelled section of the track per value of a field. A string is the field; the object adds the order.
  • FeatureColor — The canvas feature displays' color setting: a CSS color or jexl: callback in value, or a field whose values each take a range color, whose numbers each take the color of the interval between cut…
  • HicColor — The Hi-C display's color: a bin's contact count through a linear or log scale onto a named scheme.
  • LaneRows — The multi-way synteny display's rows: one lane per assembly below the anchor, so assembly is the one field, and the object is the arrangement a reader gives the lanes, written whole as every…
  • LDColor — The LD display's color setting paints the statistic the cells show, r2 or dprime, through a linear scale onto a named scheme. An unset scheme is the metric's own, reds for r² and blues for D'.
  • LDTrackDisplay — Linkage disequilibrium heatmap read from an LDTrack's pre-computed file — PLINK --r2 output and the formats that follow it.
  • LGVSyntenyColor — The LGVSyntenyDisplay's color setting: the AlignmentsColor object with field defaulting to strand, where the alignments display paints one fill.
  • LGVSyntenyDisplay — Draws a SyntenyTrack's alignments in a linear genome view, stacked and colored the way an alignments display draws reads.
  • LGVSyntenySort — The LGVSyntenyDisplay's sort setting: the AlignmentsSort object with type defaulting to length, so big syntenic blocks cluster at the top instead of interleaving with small ones.
  • LinearAlignmentsDisplay — Draws the reads of an AlignmentsTrack as a pileup under a coverage histogram.
  • LinearBasicDisplay — Draws the genes and other features of a FeatureTrack, from a BED, GFF or similar file. The display adds the gene-glyph slots (isoforms, subparts, UTRs, chevrons) to the shared canvas base.
  • LinearCanvasBaseDisplay — Holds the slots shared by the canvas-drawn linear feature displays, which stack overlapping features in rows (pileup-style glyphs).
  • LinearHicDisplay — Draws a HicTrack's contact matrix as a triangular heatmap in the linear genome view, at a bin size that follows the zoom.
  • LinearMafDisplay — The display for a MafTrack: one row per aligned species, with a conservation summary above them.
  • LinearManhattanDisplay — The Manhattan plot: the default display of a GWAS track, and one a FeatureTrack can switch to.
  • LinearMarkDisplay — A grammar of graphics over a feature, alignments or variant track: a list of marks — bars, points, rules, lines, spans, text or links — each with an encoding naming which feature fields feed its…
  • LinearMultiRowFeatureDisplay — Paints interval features as colored blocks on stacked rows partitioned by a feature attribute ("chromosome / ancestry painting").
  • LinearMultiSampleVariantDisplay — Draws the genotypes in a multi-sample VariantTrack, one row per sample or per phased haplotype.
  • LinearReferenceSequenceDisplay — Draws a ReferenceSequenceTrack as rows of bases: the forward strand, the reverse complement and the translation frames.
  • LinearScoreDisplay — Config for the worked-example score display. Attaches to any FeatureTrack.
  • LinearSyntenyDisplay — Draws a SyntenyTrack in a LinearSyntenyView, as ribbons joining the aligned regions of two stacked linear genome views.
  • LinearVariantDisplay — Extends LinearCanvasBaseDisplay for GPU-accelerated variant rendering.
  • LinearWiggleDisplay — Draws quantitative signal as bars, points, a line or a color strip (span), for one source or many; rows: 'source' draws each source in a separate row.
  • MafColor — The MAF display's color setting colors each species row's aligned cells by one field. mismatch paints a base only where it differs from the reference, base every base, identity the mean identity to…
  • MarkColor — A mark's encoding.color: one CSS color or jexl: callback for every instance, or a field through a categorical scale (a range color per value), a linear or log scale (a ramp between domainMin and…
  • MarkFacet — The mark display's facet: the Facet the feature and alignments displays take, one labelled section of the track per value of a field, plus the steps the facet runs over each section's features alone,…
  • MarkLocus — A mark's far end as a position that may lie on another sequence: pos, the feature field holding its coordinate, and chrom, the field holding its refName, as a paired record states its mate.
  • MarkSize — A mark's size in px, as color is its color: a point's diameter, a rule's thickness or a link's stroke.
  • MarkTransform — One step of a transform list, which runs over the region's features in order, each step reading what the one before it answered.
  • MultiWayGeneColor — The multi-way synteny display's gene color: a CSS color or jexl: callback in value, or a field whose values each take a range color, or whose numbers each take the color of the interval between cut…
  • MultiWayLaneLayer — One row of data drawn in every lane through that lane's own frame, from each genome's own track, on one value scale shared by every lane.
  • MultiWaySyntenyDisplay — Draws a multi-genome SyntenyTrack in a linear genome view as one lane per assembly, with ribbons joining each gene's placements in adjacent lanes.
  • QuantitativeRows — A quantitative display's rows: source is the one field a quantitative row can be, since a wiggle carries a score per base and a subtrack name and nothing else to put on rows.
  • ReadFilter — Every read filter of the alignments display in one object, its filter slot: the SAM flag masks, a minimum mapping quality, a read name, the tag filters a read has to pass every one of, and the four…
  • RibbonColor — The multi-way synteny display's ribbonColor setting: one color for every ribbon, or a field each ribbon carries: the record's strand, a measurement through its preset (identity, mapq, dnds,…
  • RowArrangement — The rows setting of a display whose rows are its own — a sample, a species — rather than the values of a field: the arrangement a reader gives them, which every product writes as a session edit to…
  • RowColor — The rowColor setting of the row displays: one categorical color channel on the row axis. field names the row attribute whose values take the colors, name (the row itself) by default, and domain/range…
  • RowGroup — One entry of the multi-row feature display's rowGroups: a row joins the group of the first entry whose match regex its name matches, and rowColor: { field: 'group' } colors the groups.
  • Rows — The rows setting of the displays that draw one row per value of a field, with the dendrogram sidebar beside them: the field, and the arrangement a reader gives the rows.
  • SampleRows — The rows of a display whose rows are the file's samples, one each, with nothing else a row could be: the multi-sample variant display and the multiple alignment display. sample is the one field, so…
  • SectionFacet — The facet of a display that stacks labelled sections, each of which a reader can hide from its chip: Facet's field and domain, and the sections hidden.
  • TagFilter — One tag a read has to carry to pass, with the value it has to hold where one is named.
  • ValueScale — The value scale of a quantitative display, written as scales.y: the wiggle plot, the alignments coverage band and the mark display, the Manhattan plot among them, each carry one, with the axis guides…
  • VariantCellColor — The multi-sample variant display's color setting: the hue of every alt-carrying genotype cell, which shadeByDosage then lightens for a heterozygote. Unset, the cells paint the genotype colors.
  • WiggleColor — The quantitative display's color: one CSS color for every bar, or score through a scale.

Internet Account

  • BaseInternetAccount — Holds an internet account's name and description, the domains it handles, and the request header it sends credentials in. Every internet account type has these slots.
  • DropboxOAuthInternetAccount — Signs requests for Dropbox files with an OAuth 2.0 token, with the Dropbox endpoints and domains filled in.
  • ExternalTokenInternetAccount — Sends a token that the user pastes in, or that an embedding portal supplies, with every request to a matching domain.
  • GoogleDriveOAuthInternetAccount — Signs requests for Google Drive files with an OAuth 2.0 token, with the Google endpoints, read-only Drive scope and domain filled in.
  • HTTPBasicInternetAccount — Prompts for a username and password, and sends them in an HTTP Basic Authorization header on requests to a matching domain.
  • OAuthInternetAccount — Signs requests to a resource that uses OAuth 2.0, fetching and refreshing the access token through the provider's authorization flow.

Root

  • FormatAbout — Holds jexl callbacks that add, rewrite or hide fields in a track's About dialog.
  • FormatDetails — Holds jexl callbacks that add, rewrite or hide fields in the feature-details panel.
  • HierarchicalConfigSchema — Sets the hierarchical track selector's starting sort order, and which categories show as folders or start collapsed. Found on the root config as configuration.hierarchical.
  • JBrowseConfiguration — Holds the app-wide settings in the configuration key of a config file, beside assemblies and tracks.
  • JBrowseRootConfig — Holds a whole JBrowse config file: the config.json of jbrowse-web, or a file with the .jbrowse extension in jbrowse-desktop.
  • LinearGenomeViewConfigSchema — Sets defaults for every linear genome view, on the root config under configuration.LinearGenomeViewPlugin.
  • PreferencesConfigSchema — Sets an admin's or embedder's defaults for user-facing preferences, found on the root config as configuration.preferences.
  • RpcOptions — Chooses whether data fetching runs on the main thread or in web workers, and how many workers to start. Found on the root config as configuration.rpc.

Track

  • AlignmentsTrack — Holds read alignments, such as a BAM or CRAM file, which LinearAlignmentsDisplay draws. The track has few settings, and the display holds most of the config and state.
  • BaseTrack — Configuration shared by all track types. Concrete tracks (FeatureTrack, AlignmentsTrack, VariantTrack, ...) extend this, so every track accepts these fields in addition to its own.
  • FeatureTrack — Holds gene and other feature annotations, such as a GFF3 or BED file, which LinearBasicDisplay usually draws.
  • GCContentTrack — GC content, or GC skew, of the assembly's sequence, computed as the view moves by a GCContentAdapter and drawn by the wiggle display.
  • GWASTrack — Holds Genome-Wide Association Study (GWAS) results, drawn as a Manhattan plot.
  • HicTrack — Holds a Hi-C contact matrix, usually a .hic file read by HicAdapter, which LinearHicDisplay draws as a triangular heatmap.
  • LDTrack — Track type for displaying pre-computed linkage disequilibrium data (e.g., from PLINK --r2 output)
  • MafTrack — Holds a multiple alignment from a MAF or TAF file, which LinearMafDisplay draws as one row per aligned species with a conservation summary above them.
  • MultiQuantitativeTrack — Holds several quantitative signals, such as one BigWig per sample, which LinearWiggleDisplay draws one row per source by default.
  • QuantitativeTrack — Holds a numeric signal such as coverage or conservation, usually from a BigWig file, which LinearWiggleDisplay draws as an XY plot or density.
  • ReferenceSequenceTrack — Holds an assembly's reference sequence, which LinearReferenceSequenceDisplay draws base by base.
  • SyntenyTrack — Holds alignments between assemblies, such as a minimap2 PAF, for the linear synteny view, the dot plot view and the linear genome view.
  • VariantTrack — Mostly similar to feature track, but has ChordDisplayType registered to it, and custom feature details in LinearVariantDisplay

View

  • SyntenyColor — The linear synteny and dotplot views' color setting, which every track in the view paints with: one color for every alignment, or a field each alignment carries — its strand, the sequence at either…
  • SyntenyOpacity — The synteny views' opacity setting, as color is their color: one opacity for every alignment, or a field each alignment carries read into opacities.