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BOAT: Basic Oligonucleotide Alignment Tool
BACKGROUND: Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788372/ https://www.ncbi.nlm.nih.gov/pubmed/19958483 http://dx.doi.org/10.1186/1471-2164-10-S3-S2 |
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author | Zhao, Shu-Qi Wang, Jun Zhang, Li Li, Jiong-Tang Gu, Xiaocheng Gao, Ge Wei, Liping |
author_facet | Zhao, Shu-Qi Wang, Jun Zhang, Li Li, Jiong-Tang Gu, Xiaocheng Gao, Ge Wei, Liping |
author_sort | Zhao, Shu-Qi |
collection | PubMed |
description | BACKGROUND: Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript expression profiles. Mapping the sequencing reads to reference genomes efficiently and effectively is one of the most critical analysis tasks. Although several tools have been developed, their performance suffers when both multiple substitutions and insertions/deletions (indels) occur together. RESULTS: We report a new algorithm, Basic Oligonucleotide Alignment Tool (BOAT) that can accurately and efficiently map sequencing reads back to the reference genome. BOAT can handle several substitutions and indels simultaneously, a useful feature for identifying SNPs and other genomic structural variations in functional genomic studies. For better handling of low-quality reads, BOAT supports a "3'-end Trimming Mode" to build local optimized alignment for sequencing reads, further improving sensitivity. BOAT calculates an E-value for each hit as a quality assessment and provides customizable post-mapping filters for further mapping quality control. CONCLUSION: Evaluations on both real and simulation datasets suggest that BOAT is capable of mapping large volumes of short reads to reference sequences with better sensitivity and lower memory requirement than other currently existing algorithms. The source code and pre-compiled binary packages of BOAT are publicly available for download at http://boat.cbi.pku.edu.cn under GNU Public License (GPL). BOAT can be a useful new tool for functional genomics studies. |
format | Text |
id | pubmed-2788372 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-27883722009-12-04 BOAT: Basic Oligonucleotide Alignment Tool Zhao, Shu-Qi Wang, Jun Zhang, Li Li, Jiong-Tang Gu, Xiaocheng Gao, Ge Wei, Liping BMC Genomics Proceedings BACKGROUND: Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript expression profiles. Mapping the sequencing reads to reference genomes efficiently and effectively is one of the most critical analysis tasks. Although several tools have been developed, their performance suffers when both multiple substitutions and insertions/deletions (indels) occur together. RESULTS: We report a new algorithm, Basic Oligonucleotide Alignment Tool (BOAT) that can accurately and efficiently map sequencing reads back to the reference genome. BOAT can handle several substitutions and indels simultaneously, a useful feature for identifying SNPs and other genomic structural variations in functional genomic studies. For better handling of low-quality reads, BOAT supports a "3'-end Trimming Mode" to build local optimized alignment for sequencing reads, further improving sensitivity. BOAT calculates an E-value for each hit as a quality assessment and provides customizable post-mapping filters for further mapping quality control. CONCLUSION: Evaluations on both real and simulation datasets suggest that BOAT is capable of mapping large volumes of short reads to reference sequences with better sensitivity and lower memory requirement than other currently existing algorithms. The source code and pre-compiled binary packages of BOAT are publicly available for download at http://boat.cbi.pku.edu.cn under GNU Public License (GPL). BOAT can be a useful new tool for functional genomics studies. BioMed Central 2009-12-03 /pmc/articles/PMC2788372/ /pubmed/19958483 http://dx.doi.org/10.1186/1471-2164-10-S3-S2 Text en Copyright ©2009 Zhao et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Proceedings Zhao, Shu-Qi Wang, Jun Zhang, Li Li, Jiong-Tang Gu, Xiaocheng Gao, Ge Wei, Liping BOAT: Basic Oligonucleotide Alignment Tool |
title | BOAT: Basic Oligonucleotide Alignment Tool |
title_full | BOAT: Basic Oligonucleotide Alignment Tool |
title_fullStr | BOAT: Basic Oligonucleotide Alignment Tool |
title_full_unstemmed | BOAT: Basic Oligonucleotide Alignment Tool |
title_short | BOAT: Basic Oligonucleotide Alignment Tool |
title_sort | boat: basic oligonucleotide alignment tool |
topic | Proceedings |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788372/ https://www.ncbi.nlm.nih.gov/pubmed/19958483 http://dx.doi.org/10.1186/1471-2164-10-S3-S2 |
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