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BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
BACKGROUND: DNA methylation is an important epigenetic modification involved in many biological processes. Bisulfite treatment coupled with high-throughput sequencing provides an effective approach for studying genome-wide DNA methylation at base resolution. Libraries such as whole genome bisulfite...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840619/ https://www.ncbi.nlm.nih.gov/pubmed/24206606 http://dx.doi.org/10.1186/1471-2164-14-774 |
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author | Guo, Weilong Fiziev, Petko Yan, Weihong Cokus, Shawn Sun, Xueguang Zhang, Michael Q Chen, Pao-Yang Pellegrini, Matteo |
author_facet | Guo, Weilong Fiziev, Petko Yan, Weihong Cokus, Shawn Sun, Xueguang Zhang, Michael Q Chen, Pao-Yang Pellegrini, Matteo |
author_sort | Guo, Weilong |
collection | PubMed |
description | BACKGROUND: DNA methylation is an important epigenetic modification involved in many biological processes. Bisulfite treatment coupled with high-throughput sequencing provides an effective approach for studying genome-wide DNA methylation at base resolution. Libraries such as whole genome bisulfite sequencing (WGBS) and reduced represented bisulfite sequencing (RRBS) are widely used for generating DNA methylomes, demanding efficient and versatile tools for aligning bisulfite sequencing data. RESULTS: We have developed BS-Seeker2, an updated version of BS Seeker, as a full pipeline for mapping bisulfite sequencing data and generating DNA methylomes. BS-Seeker2 improves mappability over existing aligners by using local alignment. It can also map reads from RRBS library by building special indexes with improved efficiency and accuracy. Moreover, BS-Seeker2 provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing the overestimation of DNA methylation levels. We also defined CGmap and ATCGmap file formats for full representations of DNA methylomes, as part of the outputs of BS-Seeker2 pipeline together with BAM and WIG files. CONCLUSIONS: Our evaluations on the performance show that BS-Seeker2 works efficiently and accurately for both WGBS data and RRBS data. BS-Seeker2 is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker2/ and the Galaxy server. |
format | Online Article Text |
id | pubmed-3840619 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-38406192013-11-27 BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data Guo, Weilong Fiziev, Petko Yan, Weihong Cokus, Shawn Sun, Xueguang Zhang, Michael Q Chen, Pao-Yang Pellegrini, Matteo BMC Genomics Software BACKGROUND: DNA methylation is an important epigenetic modification involved in many biological processes. Bisulfite treatment coupled with high-throughput sequencing provides an effective approach for studying genome-wide DNA methylation at base resolution. Libraries such as whole genome bisulfite sequencing (WGBS) and reduced represented bisulfite sequencing (RRBS) are widely used for generating DNA methylomes, demanding efficient and versatile tools for aligning bisulfite sequencing data. RESULTS: We have developed BS-Seeker2, an updated version of BS Seeker, as a full pipeline for mapping bisulfite sequencing data and generating DNA methylomes. BS-Seeker2 improves mappability over existing aligners by using local alignment. It can also map reads from RRBS library by building special indexes with improved efficiency and accuracy. Moreover, BS-Seeker2 provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing the overestimation of DNA methylation levels. We also defined CGmap and ATCGmap file formats for full representations of DNA methylomes, as part of the outputs of BS-Seeker2 pipeline together with BAM and WIG files. CONCLUSIONS: Our evaluations on the performance show that BS-Seeker2 works efficiently and accurately for both WGBS data and RRBS data. BS-Seeker2 is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker2/ and the Galaxy server. BioMed Central 2013-11-10 /pmc/articles/PMC3840619/ /pubmed/24206606 http://dx.doi.org/10.1186/1471-2164-14-774 Text en Copyright © 2013 Guo 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 | Software Guo, Weilong Fiziev, Petko Yan, Weihong Cokus, Shawn Sun, Xueguang Zhang, Michael Q Chen, Pao-Yang Pellegrini, Matteo BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data |
title | BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data |
title_full | BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data |
title_fullStr | BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data |
title_full_unstemmed | BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data |
title_short | BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data |
title_sort | bs-seeker2: a versatile aligning pipeline for bisulfite sequencing data |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840619/ https://www.ncbi.nlm.nih.gov/pubmed/24206606 http://dx.doi.org/10.1186/1471-2164-14-774 |
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