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Bismark：用于亚硫酸氢盐测序应用的灵活对齐器和甲基化调用程序。

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.

机构信息

Bioinformatics Group, The Babraham Institute, CB22 3AT, Cambridge, UK.

出版信息

Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: 10.1093/bioinformatics/btr167. Epub 2011 Apr 14.

DOI:10.1093/bioinformatics/btr167
PMID:21493656
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3102221/
Abstract

SUMMARY: A combination of bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot of a cell's epigenomic state by revealing its genome-wide cytosine methylation at single base resolution. Bismark is a flexible tool for the time-efficient analysis of BS-Seq data which performs both read mapping and methylation calling in a single convenient step. Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed. AVAILABILITY AND IMPLEMENTATION: Bismark is released under the GNU GPLv3+ licence. The source code is freely available from www.bioinformatics.bbsrc.ac.uk/projects/bismark/.

摘要

摘要：通过对 DNA 进行亚硫酸氢盐处理和高通量测序（BS-Seq）的组合，可以在单个碱基分辨率上揭示其全基因组胞嘧啶甲基化，从而捕获细胞表观基因组状态的快照。Bismark 是一种灵活的工具，可用于高效分析 BS-Seq 数据，它可以在单个方便的步骤中执行读映射和甲基化调用。它的输出区分 CpG、CHG 和 CHH 环境中的胞嘧啶，并使基础科学家能够在测序运行完成后立即可视化和解释他们的甲基化数据。

可用性和实现：Bismark 根据 GNU GPLv3+ 许可证发布。源代码可从 www.bioinformatics.bbsrc.ac.uk/projects/bismark/ 免费获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b7cd/3102221/ffbb6f6261cd/btr167f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b7cd/3102221/ffbb6f6261cd/btr167f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b7cd/3102221/ffbb6f6261cd/btr167f1.jpg

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本文引用的文献

[1]
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Nat Biotechnol. 2010-9-19

[2]
BS Seeker: precise mapping for bisulfite sequencing.

BMC Bioinformatics. 2010-4-23

[3]
Conservation and divergence of methylation patterning in plants and animals.

Proc Natl Acad Sci U S A. 2010-4-15

[4]
Establishing, maintaining and modifying DNA methylation patterns in plants and animals.

Nat Rev Genet. 2010-3

[5]
Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency.

Nature. 2010-2-25

[6]
Human DNA methylomes at base resolution show widespread epigenomic differences.

Nature. 2009-11-19

[7]
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Genome Biol. 2009

[8]
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

Nature. 2008-3-13

[9]
DNA methylation and human disease.

Nat Rev Genet. 2005-8

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