Download
Table of Contents
1 FASTA files
The public sequence resource provides all uploaded sequences as FASTA files. They can be referred to from metadata individually. We also provide a single file FASTA download.
2 Metadata
Metadata can be downloaded as Turtle RDF as a mergedmetadat.ttl which can be loaded into any RDF triple-store. We provide a Virtuoso SPARQL endpoint ourselves which can be queried from http://sparql.genenetwork.org/sparql/. Query examples can be found in our BLOG.
The Swiss Institute of Bioinformatics has included this data in https://covid-19-sparql.expasy.org/ and made it part of Uniprot.
An RDF file that includes the sequences themselves in a variation graph can be downloaded from below Pangenome RDF format.
3 Pangenome
Pangenome data is made available in multiple guises. Variation graphs (VG) provide a succinct encoding of the sequences of many genomes.
3.1 Pangenome GFA format
3.2 Pangenome in ODGI format
ODGI is a format that supports an optimized dynamic genome/graph implementation.
3.3 Pangenome RDF format
An RDF file that includes the sequences themselves in a variation graph can be downloaded from relabeledSeqs-dedup-relabeledSeqs-dedup.ttl.xz.
3.4 Pangenome Browser format
The many JSON files that are named as results/1/chunk001200.bin1.schematic.json are consumed by the Pangenome browser.
4 Log of workflow output
Including in below link is a log file of the last workflow runs.