Bread wheat genomes graph pangenome

A Giraffe and a GFA-formatted minigraph assembly of sixteen bread wheat cultivar genome assemblies.

15-wheat10+.bed.gz is the relinearised graph from gfatools gfa2bed

15-wheat10+.gfa.gz is the graph in GFA format as built by minigraph

index.min, index.dist, index.giraffe.gbz are the same graph formatted for Giraffe alignments with vg giraffe v1.34.0 or later.

vg autoindex -w giraffe -g 15-wheat10+.gfa -t 16 -T ./ -V 1 --target-mem 850G

It is possible to convert the gfa graph to vg format:

vg convert -v -g 15-wheat10+.gfa > 15-wheat10+.vg

To use the index in alignments using vg v1.34.0 or later:

vg giraffe -Z index.giraffe.gbz -m index.min -d index.dist -f your_reads.fq > mapped.gam