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DATA_SERVER.md

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igv.js Data Server Configuration

The igv.js visualization on the lineages page requires a data server from which to read the organism (currently SARS-CoV-2) reference sequence and BED files for primer sets and lineages. The URL of this data server is specified in the .env file at the project root.

This server only needs to host static files and be able to accept HTTP Range requests, so something basic like NGINX should work for this purpose.

Data Server File Paths

For the purposes of this section, we will leave off the domain of the IGV data server for clarity (e.g. a path below of <organism taxid>/config/tracks.json indicates a full URL of <IGV data server URL>/<organism taxid>/config/tracks.json).

Primer Monitor expects the data files hosted by the data server to be at the following paths:

Configuration

  • <organism taxid>/defaults.json: A JSON file containing a key "tracks", with a value of a list of the internal names of the primer sets to select by default on initial page load.

  • <organism taxid>/overrides.txt: A plain text file containing the list of lineage groups (one per line) manually added to the visualization, whether they would have been auto-selected by the algorithm or not.

  • <organism taxid>/config/tracks.json: A JSON file with key-value pairs mapping the internal name of a primer set (used in URLs), to the name a user should see on the site (e.g. "ARTIC_v4": "ARTIC v4"). The list of available primer sets is also obtained from the list of key-value pairs in this file.

  • <organism taxid>/config/lineage_sets.json: A JSON file with key-value pairs mapping the internal name of a lineage set (used in URLs), to the name a user should see on the site (e.g. "BA.2": "BA.2.*"). The list of available lineage sets is also obtained from the list of key-value pairs in this file.

Primer sets

  • <organism taxid>/primer_sets_status/<primer set name>/<lineage group name>.bed: A BED file (minimum 9 columns) containing a record for each primer in the primer set. The color is used to mark whether the primer is affected by a variant in the specified lineage group.

  • <organism taxid>/primer_sets_bed/<primer set name>.bed: A BED file containing the raw primer annotations for each primer in the primer set.

  • <organism taxid>/primer_sets_fasta/<primer set name>.fasta: A FASTA file containing the raw primer sequences for each primer in the primer set.

Lineage sets

  • <organism taxid>/lineage_sets/<lineage set>.txt: A plain text file listing the Pango lineages in the database comprising a lineage set. The filenames match the internal names from lineage_sets.json.

  • <organism taxid>/lineage_variants/<lineage set>.bed: A BED file listing the variants detected in the specified lineage set. The filenames match the internal names from lineage_sets.json.

Reference sequence

  • <organism taxid>/ref/<genbank accession>.fasta: The reference sequence of the SARS-CoV-2 virus in FASTA format. For SARS-CoV-2, <genbank accession> is NC_045512.2.
  • <organism taxid>/ref/<genbank accession>.fasta.fai: An index of the FASTA reference sequence.
  • <organism taxid>/ref/<genbank accession>.gff3: A GFF3 file containing genome annotations.