Human exome

A human exome sequencing dataset on hg38.

The NA12878 CEU exome from the 1000 Genomes Project — a CRAM alignments track on GRCh38 — beside NCBI RefSeq genes, opened at a gene locus on chromosome 1.

The CRAM is fetched over HTTP range requests straight from S3, so there is no server-side component. Config slots: CramAdapter, AlignmentsTrack. On alignments data this size, turn on the web worker RPC.

View source — 43 lines

import { LinearGenomeView } from '@jbrowse/react-linear-genome-view2'

// managed API: props are initial values, the component owns the engine
export default function HumanExomeExample() {
  return (
    <LinearGenomeView
      assembly={{
        name: 'GRCh38',
        uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz',
        aliases: ['hg38'],
        refNameAliases: {
          uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt',
        },
      }}
      tracks={[
        {
          type: 'FeatureTrack',
          trackId: 'ncbi-refseq-genes',
          name: 'NCBI RefSeq Genes',
          assemblyNames: ['GRCh38'],
          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',
          },
        },
        {
          type: 'AlignmentsTrack',
          trackId: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome',
          name: 'NA12878 Exome',
          assemblyNames: ['GRCh38'],
          adapter: {
            type: 'CramAdapter',
            uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram',
          },
        },
      ]}
      init={{
        loc: '1:100,987,269..100,987,368',
        tracks: ['NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome'],
      }}
    />
  )
}