Equus caballus Genome sequencing and assembly

The current reference assembly for the domestic horse Equus caballus was published in 2009. This assembly used Sanger (first-generation) sequencing along with bacterial artificial chromosomes (BACs) to produce an assembly with 112kb contig N50 and 46Mb scaffold N50. Since 2009, there have been enormous advances in sequencing technology, bringing the cost and time required for sequencing down by more than a factor of 10,000. We used the existing Sanger sequence data along with several of these new technologies to assemble a new reference genome. Illumina HiSeq short reads increased average assembly read depth six-fold, resulting in fewer mis-calls. We used CHiCago and Hi-C long-insert libraries to improve scaffold assembly, nearly doubling the scaffold N50 and increasing the amount of sequence assigned to chromosomes. Gap-filling with PacBio long reads greatly increased contig sizes. We used a 10x Chromium library to identify and phase variants. The final assembly has 4,493kb contig N50, 85Mb scaffold N50, and 70Mb more sequence assigned to chromosomes.