PT  - JOURNAL ARTICLE
AU  - Lynsey K. Whitacre
AU  - Polyana C. Tizioto
AU  - JaeWoo Kim
AU  - Tad S. Sonstegard
AU  - Steven G. Schroeder
AU  - Leeson J. Alexander
AU  - Juan F. Medrano
AU  - Robert D. Schnabel
AU  - Jeremy F. Taylor
AU  - Jared E. Decker
TI  - What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual
AID  - 10.1101/022731
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 022731
4099  - http://biorxiv.org/content/early/2015/07/17/022731.short
4100  - http://biorxiv.org/content/early/2015/07/17/022731.full
AB  - Next-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped. We generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species. We demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of infectious or symbiotic organisms.