Progress on Developing SheepGenomesDB for the Ovine Research Community

SheepGenomesDB is an electronic warehouse containing sequence variants called from the expanding collection of sheep genomes being generated across our research community. Through the application of a single harmonised pipeline for read QC, mapping, variant detection and annotation, SheepGenomesDB makes available variant collections derived in a standardised manner. Here, we present the eligibility criteria for genome data that may potentially contribute to the project, including data access considerations, metadata requirements, depth of coverage and data formats. We present the flow of data, from data deposition and storage using the Short Read Archive to aspects of variant accessioning and functional annotation supported by the European Variation Archive. The first analysis run has been completed, with read mapping and variant calling performed for 350 sheep genomes from nearly 50 breeds. This identified in excess of 25 million SNP. Collections of both unfiltered and filtered variants are being passed to the European Variant Archive, which will serve as an important interface to the user community. The creators view SheepGenomesDB as an essential resource for researchers interested in gene mutation discovery, imputation as it relates to genome-wide association and genomic prediction as well as investigations into genome evolution, domestication and the consequences of selection.