Human demo (hg38)

A richer hg38 session: genes, repeats, exome alignments, variants, and conservation.

A real-world hg38 session, opened at the SHH locus, carrying the kinds of track a production embed runs at once:

NCBI RefSeq genes (GFF3+tabix) with a TrixTextSearchAdapter, so typing a gene symbol in the location box jumps there
Repeats from a BigBed
NA12878 exome alignments (CRAM, 1000 Genomes)
1000 Genomes variant calls (VCF+tabix)
phyloP100way conservation as a BigWig

Every file is fetched over HTTP range requests from public buckets, so there is no server-side component. It is the same <JBrowse> as the basic example with a fuller assemblies/tracks. On alignments data this heavy, turn on the web worker RPC.

View source — 113 lines

import { JBrowse } from '@jbrowse/react-app2'

// { name, uri } shorthand + a refNameAliases file so tracks using `1`/`chr1`
// both resolve. Core infers BgzipFastaAdapter from the .fa.gz extension.
const assemblies = [
  {
    name: 'GRCh38',
    aliases: ['hg38'],
    uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
    refNameAliases: {
      uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt',
    },
  },
]

const tracks = [
  {
    type: 'FeatureTrack',
    trackId: 'genes',
    name: 'NCBI RefSeq Genes',
    assemblyNames: ['GRCh38'],
    category: ['Genes'],
    adapter: {
      type: 'Gff3TabixAdapter',
      uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz',
    },
    textSearching: {
      textSearchAdapter: {
        type: 'TrixTextSearchAdapter',
        textSearchAdapterId: 'gff3tabix_genes-index',
        ixFilePath: {
          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix',
        },
        ixxFilePath: {
          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx',
        },
        metaFilePath: {
          uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json',
        },
        assemblyNames: ['GRCh38'],
      },
    },
  },
  {
    type: 'FeatureTrack',
    trackId: 'repeats_hg38',
    name: 'Repeats',
    assemblyNames: ['GRCh38'],
    category: ['Annotation'],
    adapter: {
      type: 'BigBedAdapter',
      uri: 'https://jbrowse.org/genomes/GRCh38/repeats.bb',
    },
  },
  {
    type: 'AlignmentsTrack',
    trackId: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome',
    name: 'NA12878 Exome',
    assemblyNames: ['GRCh38'],
    category: ['1000 Genomes', 'Alignments'],
    adapter: {
      type: 'CramAdapter',
      uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram',
    },
  },
  {
    type: 'VariantTrack',
    trackId:
      'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf',
    name: '1000 Genomes Variant Calls',
    assemblyNames: ['GRCh38'],
    category: ['1000 Genomes', 'Variants'],
    adapter: {
      type: 'VcfTabixAdapter',
      uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz',
    },
  },
  {
    type: 'QuantitativeTrack',
    trackId: 'hg38.100way.phyloP100way',
    name: 'hg38.100way.phyloP100way',
    category: ['Conservation'],
    assemblyNames: ['GRCh38'],
    adapter: {
      type: 'BigWigAdapter',
      uri: 'https://hgdownload.soe.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw',
    },
  },
]

export default function HumanDemo() {
  return (
    <JBrowse
      assemblies={assemblies}
      tracks={tracks}
      views={[
        {
          type: 'LinearGenomeView',
          init: {
            loc: 'chr7:155,799,529..155,812,871',
            assembly: 'hg38',
            tracks: [
              'genes',
              'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome',
              'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf',
              'hg38.100way.phyloP100way',
            ],
          },
        },
      ]}
    />
  )
}