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 al...

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Autores principales:	Stephen M Rumble, Phil Lacroute, Adrian V Dalca, Marc Fiume, Arend Sidow, Michael Brudno
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/8e723676333a4ed097d879bbc3dd5e18
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spelling	oai:doaj.org-article:8e723676333a4ed097d879bbc3dd5e182021-11-25T05:42:23ZSHRiMP: accurate mapping of short color-space reads.1553-734X1553-735810.1371/journal.pcbi.1000386https://doaj.org/article/8e723676333a4ed097d879bbc3dd5e182009-05-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19461883/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The 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.Stephen M RumblePhil LacrouteAdrian V DalcaMarc FiumeArend SidowMichael BrudnoPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 5, p e1000386 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Stephen M Rumble Phil Lacroute Adrian V Dalca Marc Fiume Arend Sidow Michael Brudno SHRiMP: accurate mapping of short color-space reads.
description	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.
format	article
author	Stephen M Rumble Phil Lacroute Adrian V Dalca Marc Fiume Arend Sidow Michael Brudno
author_facet	Stephen M Rumble Phil Lacroute Adrian V Dalca Marc Fiume Arend Sidow Michael Brudno
author_sort	Stephen M Rumble
title	SHRiMP: accurate mapping of short color-space reads.
title_short	SHRiMP: accurate mapping of short color-space reads.
title_full	SHRiMP: accurate mapping of short color-space reads.
title_fullStr	SHRiMP: accurate mapping of short color-space reads.
title_full_unstemmed	SHRiMP: accurate mapping of short color-space reads.
title_sort	shrimp: accurate mapping of short color-space reads.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/8e723676333a4ed097d879bbc3dd5e18
work_keys_str_mv	AT stephenmrumble shrimpaccuratemappingofshortcolorspacereads AT phillacroute shrimpaccuratemappingofshortcolorspacereads AT adrianvdalca shrimpaccuratemappingofshortcolorspacereads AT marcfiume shrimpaccuratemappingofshortcolorspacereads AT arendsidow shrimpaccuratemappingofshortcolorspacereads AT michaelbrudno shrimpaccuratemappingofshortcolorspacereads
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SHRiMP: accurate mapping of short color-space reads.

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