Download

We provide download links for a number of different files to allow researchers to carry out their own analysis.

Pangenome

FASTA file containing nucleotide sequences of all reference-derived contigs (chromosomes and scaffolds) plus all other pangenomic contigs.

pangenome.fasta

GFF3 file containing all genomic features of the pangenome (annotation file for pangenome.fasta above).

pangenome.gff3

Complete PAV (presence/absence variation) binary matrix for all Watkins accessions, covering both core and variable genes.

pangenome.pav.csv

Subset of the pangenome.fasta for contigs generated through de novo assembly of all unmapped reads from the Watkins collection.

additional_contigs.fasta

Subset of the pangenome.gff3 for contigs generated through de novo assembly of all unmapped reads from the Watkins collection.

additional_contigs.gff3

Subset of the pangenome.pav.csv for contigs generated through de novo assembly of all unmapped reads from the Watkins collection.

additional_contigs.pav.csv

CDS nucleotide sequences for all gene models in the pangenome.gff3.

pangenome.cds.fa

Predicted protein sequences for all gene models in the pangenome.gff3.

pangenome.protein.fa