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Slider—maximum use of probability information for alignment of short sequence reads and SNP detection
Motivation: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will intr...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638935/ https://www.ncbi.nlm.nih.gov/pubmed/18974170 http://dx.doi.org/10.1093/bioinformatics/btn565 |
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author | Malhis, Nawar Butterfield, Yaron S. N. Ester, Martin Jones, Steven J. M. |
author_facet | Malhis, Nawar Butterfield, Yaron S. N. Ester, Martin Jones, Steven J. M. |
author_sort | Malhis, Nawar |
collection | PubMed |
description | Motivation: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files. Results: Compared with other aligners, Slider has higher alignment accuracy and efficiency. In addition, given that Slider matches bases with probabilities other than the most probable, it significantly reduces the percentage of base mismatches. The result is that its SNP predictions are more accurate than other SNP prediction approaches used today that start from the most probable sequence, including those using base quality. Contact: nmalhis@bcgsc.ca Supplementary information and availability: http://www.bcgsc.ca/platform/bioinfo/software/slider |
format | Text |
id | pubmed-2638935 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-26389352009-02-25 Slider—maximum use of probability information for alignment of short sequence reads and SNP detection Malhis, Nawar Butterfield, Yaron S. N. Ester, Martin Jones, Steven J. M. Bioinformatics Original Papers Motivation: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files. Results: Compared with other aligners, Slider has higher alignment accuracy and efficiency. In addition, given that Slider matches bases with probabilities other than the most probable, it significantly reduces the percentage of base mismatches. The result is that its SNP predictions are more accurate than other SNP prediction approaches used today that start from the most probable sequence, including those using base quality. Contact: nmalhis@bcgsc.ca Supplementary information and availability: http://www.bcgsc.ca/platform/bioinfo/software/slider Oxford University Press 2009-01-01 2008-10-30 /pmc/articles/PMC2638935/ /pubmed/18974170 http://dx.doi.org/10.1093/bioinformatics/btn565 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Papers Malhis, Nawar Butterfield, Yaron S. N. Ester, Martin Jones, Steven J. M. Slider—maximum use of probability information for alignment of short sequence reads and SNP detection |
title | Slider—maximum use of probability information for alignment of short sequence reads and SNP detection |
title_full | Slider—maximum use of probability information for alignment of short sequence reads and SNP detection |
title_fullStr | Slider—maximum use of probability information for alignment of short sequence reads and SNP detection |
title_full_unstemmed | Slider—maximum use of probability information for alignment of short sequence reads and SNP detection |
title_short | Slider—maximum use of probability information for alignment of short sequence reads and SNP detection |
title_sort | slider—maximum use of probability information for alignment of short sequence reads and snp detection |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638935/ https://www.ncbi.nlm.nih.gov/pubmed/18974170 http://dx.doi.org/10.1093/bioinformatics/btn565 |
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