whole-genome sequencing for heterogeneous stock rat founder individual
41.81x coverage Illumina short read whole genome sequence data for the 8 heterogeneous stock rat founders. Methods for high coverage WGS sequencing The Agencourt DNAdvance Kit (Beckman Coulter Life Sciences, Indianapolis, IN) was used to extract DNA from the small intestine or liver tissues of eight inbred HS rat founders. Next, DNA libraries were prepared according to the manufacturer's protocol using KAPA HyperPrep Kits (Roche, Basel, Switzerland). The DNA were then sequenced with Illumina NovaSeq 6000 to obtain 41.81x coverage 150 bp paired-end reads at the University of California San Diego Institute for Genomic Medicine Genomics Center. Methods for high coverage WGS sequence mapping At the sequence quality control step, BBDuk was used to trim the adapters and poly-G tails with length greater than 50 bp (Bushnell). We then aligned the sequences to the reference genome and did quality control on aligned reads with BWA-mem and Samtools (Li, Danecek et al.). We then used Genome Analysis Toolkit (GATK) (Van der Auwera and O'Connor) indel realignment to further polish the mapped sequences.