SHRiMP: accurate mapping of short color-space reads. 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

References in zbMATH (referenced in 15 articles , 1 standard article )

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  1. Gagie, Travis; Manzini, Giovanni; Valenzuela, Daniel: Compressed spaced suffix arrays (2017)
  2. Girotto, Samuele; Comin, Matteo; Pizzi, Cinzia: Metagenomic reads binning with spaced seeds (2017)
  3. Girotto, Samuele; Comin, Matteo; Pizzi, Cinzia: Fast spaced seed hashing (2017)
  4. Liu, Yongchao; Schmidt, Bertil: CUSHAW suite: parallel and efficient algorithms for NGS read alignment (2017)
  5. Shen, Carol; Shen, Tony; Lin, Jimmy: Comparative assessment of alignment algorithms for NGS data: features, considerations, implementations, and future (2017)
  6. Picardi, Ernesto (ed.): RNA bioinformatics (2015)
  7. Egidi, Lavinia; Manzini, Giovanni: Design and analysis of periodic multiple seeds (2014)
  8. Egidi, Lavinia; Manzini, Giovanni: Better spaced seeds using quadratic residues (2013)
  9. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  10. Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq: A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes (2012) ioport
  11. David, Matei; Dzamba, Misko; Lister, Dan; Ilie, Lucian; Brudno, Michael: Shrimp2: sensitive yet practical short read mapping (2011) ioport
  12. Homer, Nils; Nelson, Stanley F.; Merriman, Barry: Local alignment of generalized k-base encoded DNA sequence (2010) ioport
  13. Noé, Laurent; Gîrdea, Marta; Kucherov, Gregory: Designing efficient spaced seeds for SOLiD read mapping (2010)
  14. Ratan, Aakrosh; Zhang, Yu; Hayes, Vanessa M.; Schuster, Stephan C.; Miller, Webb: Calling SNPs without a reference sequence (2010) ioport
  15. Homer, Nils; Merriman, Barry; Nelson, Stanley F.: Local alignment of two-base encoded DNA sequence (2009) ioport