Simultaneous alignment of short reads against multiple genomes
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1,176 citations
Cites methods from "Simultaneous alignment of short rea..."
...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]....
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...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]....
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References
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"Simultaneous alignment of short rea..." refers methods in this paper
...Different approaches for fast mapping of short reads have been suggested, including methods for indexing substrings of either the short reads or the reference sequence with the use of k-mers or spaced seeds (academic tools such as Bowtie, BWA, CloudBurst, MAQ, MOM, MosaikAligner, mrFAST, mrsFAST, Pash, PASS, PatMaN, RazorS, RMAP, SeqMap, SHRiMP, SliderII, SOAP, SOAP2, ssaha2 [2,11-28], and commercial tools such as ZOOM [29])....
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20,335 citations
"Simultaneous alignment of short rea..." refers background or methods in this paper
..., BurrowsWheeler indexing [16]), the latter are usually geared toward ungapped alignments and are not easily extendable to nonlinear structures imposed by multiple genomes....
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...It has been reported that the current high demand for rapid alignments, to accommodate the flood of data generated by efforts such as the 1000 Genomes Project, can be met with new indexing strategies [16]....
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...Different approaches for fast mapping of short reads have been suggested, including methods for indexing substrings of either the short reads or the reference sequence with the use of k-mers or spaced seeds (academic tools such as Bowtie, BWA, CloudBurst, MAQ, MOM, MosaikAligner, mrFAST, mrsFAST, Pash, PASS, PatMaN, RazorS, RMAP, SeqMap, SHRiMP, SliderII, SOAP, SOAP2, ssaha2 [2,11-28], and commercial tools such as ZOOM [29])....
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...SOAP and MAQ were previously compared with bowtie [16], but with a human target....
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"Simultaneous alignment of short rea..." refers methods in this paper
...The initial resequencing of Caenorhabditis elegans and Arabidopsis thaliana (Arabidopsis) strains with Illumina reads [1,2] was recently complemented by genome sequences of several human individuals, generated with data derived from technologies from Illumina (San Diego, CA, USA), Applied Biosystems (Foster City, CA, USA), and Helicos (Cambridge, MA, USA) [3-10]....
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