Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery.

ABSTRACT:

Background

The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references.

Results

We augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-a

SUBMITTER: Crysnanto D 

PROVIDER: S-EPMC7385871 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature