Validation of synthetic long reads for use in constructing variant graphs for dairy cattle breeding M Keehan and C Couldrey Research and Development, Livestock Improvment Corporation, Hamilton, New Zealand 3240 mkeehan@lic.co.nz (Corresponding Author) Recently 10x Genomics have released 10x GemCode Technology which makes cost effective synthetic long read data available to animal breeders. In this paper we report quality metrics from a validation study of 10x Genomics data obtained from seven New Zealand dairy bulls. We use two separate 10x Genomics pipelines with the aim of determining which approach is best for use in the future for variant graph construction. The mapping/variant calling pipeline (Longranger) is tested as well as the parameter free, diploid Supernova de novo assembly pipeline to individually assemble the seven genomes. Longranger provides excellent Single Nucleotide Polymorphism (SNP) discovery, phasing and genotyping. The Supernova pipeline easily generates unbiased contigs of a reasonable quality. The 10x Genomics platform together with Longranger and Supernova assembly pipelines provide an excellent value for money approach for both variant detection and de novo assembly. Keywords: sequencing, Sequence – gene annotation, assembly.


Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 339, 2018
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