BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.

Bioinformatics
Elena Y HarrisStefano Lonardi

Abstract

We introduce BRAT-BW, a fast, accurate and memory-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform). BRAT-BW is significantly more memory efficient and faster on longer reads than current state-of-the-art tools for BS-seq data, without compromising on accuracy. BRAT-BW is a part of a software suite for genome-wide single base-resolution methylation data analysis that supports single and paired-end reads and includes a tool for estimation of methylation level at each cytosine. The software is available in the public domain at http://compbio.cs.ucr.edu/brat/.

References

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Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Dec 25, 2009·Bioinformatics·Elena Y HarrisStefano Lonardi
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Citations

Sep 19, 2012·Nature Reviews. Genetics·Christoph Bock
Aug 24, 2013·BMC Bioinformatics·Shuying SunXiaoqing Yu
Nov 23, 2013·BMC Bioinformatics·Changjin HongWilliam Evan Johnson
Nov 12, 2013·BMC Genomics·Weilong GuoMatteo Pellegrini
Jun 14, 2013·Plant Methods·Thomas J Hardcastle
May 21, 2014·PloS One·Andrea ManconiLuciano Milanesi
Jan 16, 2014·Nucleic Acids Research·Yutaka SaitoToutai Mituyama
May 20, 2014·Advances in Bioinformatics·Hong TranLiqing Zhang
Mar 11, 2016·BMC Bioinformatics·Nicola PrezzaAlberto Policriti
Sep 1, 2015·Bioinformatics·Shengjie GaoLars Bolund
Jul 4, 2015·GigaScience·Shengjie GaoKarina D Sørensen
May 29, 2014·Briefings in Bioinformatics·Swarnaseetha AdusumalliTouati Benoukraf
May 7, 2016·Bioinformatics·Elena Y HarrisStefano Lonardi
Jul 1, 2016·Epigenetics & Chromatin·Wai-Shin YongPao-Yang Chen
Jun 14, 2013·International Journal of Molecular Sciences·Man-Wah LiHon-Ming Lam
Oct 1, 2016·Cancer Informatics·Sunny TianShuying Sun
Dec 21, 2018·Journal of Bioinformatics and Computational Biology·Joungmin ChoiHeejoon Chae
Nov 2, 2018·Nature Communications·Cuijun ZhangJian-Kang Zhu
Sep 10, 2019·Cancer Informatics·Shuying SunBrittany Enfield
May 17, 2017·Proceedings of the National Academy of Sciences of the United States of America·Zhaobo LangJian-Kang Zhu
May 16, 2019·BioData Mining·Lillian Sun, Shuying Sun
Dec 12, 2018·BMC Bioinformatics·Seokjun SoeHeejoon Chae
Oct 27, 2017·BMC Bioinformatics·Min LiFang-Xiang Wu
Mar 8, 2021·Genomics·Nasibeh ChenaraniJavad Zahiri
Mar 17, 2018·Progress in Retinal and Eye Research·Ximena Corso-DíazAnand Swaroop
Jun 29, 2021·Bioinformatics·Zhiqiang ZhangJiantao Shi
Aug 28, 2021·Genome Biology·Mohammed AlserSerghei Mangul

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