Whole Genome Sequencing of a French Bulldog

An Illumina TruSeq PCR-free DNA library with ~450 bp insert size of a brown French Bulldog was prepared. We collected 149 million 2 × 125 bp paired-end reads or 14× coverage on a HiSeq2500 instrument (Illumina, San Diego, CA, USA). The reads were mapped to the dog reference genome assembly CanFam3.1 and aligned as described [20 (link)]. Briefly, after trimming adaptor sequences and low-quality bases at the ends of reads with FASTP [21 (link)], BWA version 0.7.13 [22 (link)] was used for the alignment to the canine reference genome. Samtools version 0.1.18 [23 (link)] was used to sort the aligned reads by coordinates, and to produce bam-files. Duplicates were marked with Picard tools [24 ]. The sequence data were submitted to the European Nucleotide Archive with the study accession PRJEB16012 and sample accession SAMEA4504835.