title: What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.
  
  
  CONCLUSIONS
  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 parasitic or commensal organisms.
authors.affiliation: Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. lwhitacre@mail.missouri.edu.|Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. lwhitacre@mail.missouri.edu.
authors.forename: Lynsey K
authors.initials: LK
authors.lastname: Whitacre
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. polytizioto@yahoo.com.br.|Embrapa Southeast Livestock, São Carlos, São Paulo, 13560-970, Brazil. polytizioto@yahoo.com.br.
authors.forename: Polyana C
authors.initials: PC
authors.lastname: Tizioto
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. kijae@missouri.edu.
authors.forename: JaeWoo
authors.initials: J
authors.lastname: Kim
authors.affiliation: Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA. tad.sonstegard@ars.usda.gov.|Recombinetics Inc., 1246 University Ave W #301, St Paul, MN, 55104, USA. tad.sonstegard@ars.usda.gov.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA. steven.schroeder@ars.usda.gov.
authors.forename: Steven G
authors.initials: SG
authors.lastname: Schroeder
authors.affiliation: USDA-ARS (retired), LARRL, Fort Keogh Miles City, Montana, 59301, USA.
authors.forename: Leeson J
authors.initials: LJ
authors.lastname: Alexander
authors.affiliation: Department of Animal Science, University of California-Davis, Davis, CA, 95616, USA. jfmedrano@ucdavis.edu.
authors.forename: Juan F
authors.initials: JF
authors.lastname: Medrano
authors.affiliation: Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. schnabelr@missouri.edu.|Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. schnabelr@missouri.edu.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Schnabel
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. taylorjerr@missouri.edu.
authors.forename: Jeremy F
authors.initials: JF
authors.lastname: Taylor
authors.affiliation: Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. DeckerJE@missouri.edu.|Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. DeckerJE@missouri.edu.
authors.forename: Jared E
authors.initials: JE
authors.lastname: Decker
mesh_terms: D000465:Algorithms; D000818:Animals; D002417:Cattle / Q000235:genetics*; D004247:DNA / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D012313:RNA / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000662:veterinary*
chemical_list: D012313:RNA; D004247:DNA