SHRiMP: Accurate Mapping of Short Color-space Reads

By Stephen M. Rumble, P. Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno. PLoS Comput. Biol., 2009

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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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8f92cee2ec7c1338e561757326dda535c339d6b1

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Citations in the corpus

Assembly Algorithms for Next-Generation Sequencing Data (2010, neutral): “Published software includes SOAP [68,69], MAQ [70], Bowtie [71], RMAP [72], CloudBurst [73], SHRiMP [74], RazerS [75], PerM [76], segemehl [77], GenomeMapper [78], and BOAT [79].”
BFAST: An Alignment Tool for Large Scale Genome Resequencing (2009, neutral): “[23].”
ChIP-Seq: advantages and challenges of a maturing technology (2009, methodology): “For the SOLiD di-base sequencing technology, in which two consecutive bases are read at a time, modified aligners have been develope”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, methodology): “A variety of tools that are beyond the scope of this paper have been developed for alignment and de novo assembly of short reads (for examples, see Warren et al. 2007; Dohm et al. 2007; Jeck et al. 2007; De Bona et al. 2008; Chaisson and Pevzner 2008; Li et al. 2008a; Smith et al. 2008; Zerbino and ”
A survey of sequence alignment algorithms for next-generation sequencing (2010, methodology): “The q-gram filter, as is implemented in SHRiMP [29]”
From RNA-seq reads to differential expression results (2010, methodology): “Current aligners enable fast heuristic matching by using either hash tables [19-22] or the Burrows Wheeler transform (BWT) [23-25].”
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory (2012, methodology): “The relationship between many existing alignment methods [1,3-5,10-23] is qualitatively illustrated in Figure 1.”
Colistin Resistance in Acinetobacter baumannii Is Mediated by Complete Loss of Lipopolysaccharide Production (2010, methodology): “the SHRiMP program (27) (average read depth, 110), as described previously”
SNP Discovery through Next-Generation Sequencing and Its Applications (2012, methodology): “For example, in aligning 2 × 13,326,195 paired-end reads (76 bp) from The Cancer Genome Atlas project (SRR018643) [64], SHRiMP [65] took 1,065 hrs with a peak memory footprint of 12 gigabytes to achieve the mapping of 81% of the reads to the human genome reference whereas Bowtie used 2.9 gigabytes…”
Fast and accurate long-read alignment with Burrows–Wheeler transform (2010, background): “Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk Received on September 19, 2009; revised on November 24, 2009; accepted on December 16, 2009”
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping (2013, methodology): “The hash-based aligners, Eland (AJ Cox, Illumina, San Diego), MAQ (Li et al. 2008), mrFAST/mrsFast (Alkan et al. 2009; Hach et al. 2010), SHRiMP (Rumble et al. 2009; David et al. t2011), and ZOOM (Lin et al. 2008; Zhang et al. 2010) hash the reads and fit these hashes to the reference genome, while ”