title: SHRiMP: accurate mapping of short color-space reads.
abstract: The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25-70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp.
authors.affiliation: Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Rumble
authors.forename: Phil
authors.initials: P
authors.lastname: Lacroute
authors.forename: Adrian V
authors.initials: AV
authors.lastname: Dalca
authors.forename: Marc
authors.initials: M
authors.lastname: Fiume
authors.forename: Arend
authors.initials: A
authors.lastname: Sidow
authors.forename: Michael
authors.initials: M
authors.lastname: Brudno
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D015233:Models, Statistical; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014561:Urochordata / Q000235:genetics