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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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-05-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1000386 |
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| _version_ | 1850127124882522112 |
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| 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 |
| collection | DOAJ |
| 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 |
| id | doaj-art-8e723676333a4ed097d879bbc3dd5e18 |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2009-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-8e723676333a4ed097d879bbc3dd5e182025-08-20T02:33:44ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582009-05-0155e100038610.1371/journal.pcbi.1000386SHRiMP: accurate mapping of short color-space reads.Stephen M RumblePhil LacrouteAdrian V DalcaMarc FiumeArend SidowMichael BrudnoThe 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.https://doi.org/10.1371/journal.pcbi.1000386 |
| spellingShingle | Stephen M Rumble Phil Lacroute Adrian V Dalca Marc Fiume Arend Sidow Michael Brudno SHRiMP: accurate mapping of short color-space reads. PLoS Computational Biology |
| title | 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_short | SHRiMP: accurate mapping of short color-space reads. |
| title_sort | shrimp accurate mapping of short color space reads |
| url | https://doi.org/10.1371/journal.pcbi.1000386 |
| work_keys_str_mv | AT stephenmrumble shrimpaccuratemappingofshortcolorspacereads AT phillacroute shrimpaccuratemappingofshortcolorspacereads AT adrianvdalca shrimpaccuratemappingofshortcolorspacereads AT marcfiume shrimpaccuratemappingofshortcolorspacereads AT arendsidow shrimpaccuratemappingofshortcolorspacereads AT michaelbrudno shrimpaccuratemappingofshortcolorspacereads |