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Fast and accurate read mapping with approximate seeds and multiple backtracking
We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2–4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627565/ https://www.ncbi.nlm.nih.gov/pubmed/23358824 http://dx.doi.org/10.1093/nar/gkt005 |
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author | Siragusa, Enrico Weese, David Reinert, Knut |
author_facet | Siragusa, Enrico Weese, David Reinert, Knut |
author_sort | Siragusa, Enrico |
collection | PubMed |
description | We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2–4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai. |
format | Online Article Text |
id | pubmed-3627565 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-36275652013-04-17 Fast and accurate read mapping with approximate seeds and multiple backtracking Siragusa, Enrico Weese, David Reinert, Knut Nucleic Acids Res Methods Online We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2–4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai. Oxford University Press 2013-04 2013-01-28 /pmc/articles/PMC3627565/ /pubmed/23358824 http://dx.doi.org/10.1093/nar/gkt005 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Siragusa, Enrico Weese, David Reinert, Knut Fast and accurate read mapping with approximate seeds and multiple backtracking |
title | Fast and accurate read mapping with approximate seeds and multiple backtracking |
title_full | Fast and accurate read mapping with approximate seeds and multiple backtracking |
title_fullStr | Fast and accurate read mapping with approximate seeds and multiple backtracking |
title_full_unstemmed | Fast and accurate read mapping with approximate seeds and multiple backtracking |
title_short | Fast and accurate read mapping with approximate seeds and multiple backtracking |
title_sort | fast and accurate read mapping with approximate seeds and multiple backtracking |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627565/ https://www.ncbi.nlm.nih.gov/pubmed/23358824 http://dx.doi.org/10.1093/nar/gkt005 |
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