Published February 15, 2022 | Version 1.0
Dataset Open

Bread wheat genomes graph pangenome

Authors/Creators

  • 1. School of Biological Sciences, The University of Western Australia, Perth 6009, Australia
  • 2. DIADE, Univ Montpellier, CIRAD, IRD, Montpellier 34830, France
  • 3. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
  • 4. Bioversity International, Parc Scientifique Agropolis II, Montpellier 34397, France
  • 5. Centre for Comparative Genomics, Murdoch University, 90 South Street, WA6150 Murdoch, Australia
  • 6. School of Veterinary and Life Sciences, Murdoch University, 90 South Street, WA6150 Murdoch, Australia

Description

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

 

Notes

This work is funded by the Australia Research Council (Projects DP210100296, DP200100762, and DE210100398). This work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

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