Mapping the Original Sanger Sequencing Reads from “Twilight” to the Reference Equine Genome Assembly They Produced

Approximately 30 million Sanger reads were generated from the Thoroughbred mare Twilight to produce the reference Equine genome assembly (EquCab2, Wade et al 2009).  The Equine research community has used this quality reference genome successfully for several years.  Regardless of species, however, errors in reference assemblies are inevitable and will result in a small number of deceptive findings in variant detection and gene mapping efforts.  Presented here is the result of work to map the original Sanger reads back to the reference equine genome assembly for the purpose of aiding efforts to study sequence variants and potential ambiguities.   

The Sanger reads associated with the Equine Genome Project were downloaded from the NCBI Trace Archive.  The reads were base called via phred and quality trimmed at the ends.  Reads longer than 200 bp were mapped to the Equine genome using BWA-SW, those shorter were mapped using BWA.  The resulting mapped datasets were combined into a single binary alignment map file, which is made available for use through a web-based interface.

In this work, we have mapped the original Sanger reads used to produce the EquCab2 reference to that assembly. The resulting binary alignment map file is provided as source data for use in evaluating the confidence of reference nucleotide calls andverifying sequence variants identified relative to the reference equine genome. The binary alignment map file is available as an open resource via the Intrepid Bioinformatics data management system and can be browsed through their version of the Integrative Genomics Viewer.