Advance Access publication April 14, 2011 | Felix Krueger* and Simon R. Andrews
Bismark is a flexible and efficient tool for analyzing bisulfite sequencing (BS-Seq) data, which captures genome-wide cytosine methylation at single base resolution. It performs both read mapping and methylation calling in a single step, discriminating between CpG, CHG, and CHH contexts. Bismark addresses the computational challenges of bisulfite mapping by running four parallel alignment processes to determine the strand origin of each read. This approach ensures accurate and unbiased methylation analysis, even for partial methylation. The tool is released under the GNU GPLv3+ license and is freely available from the Bioinformatics Group at the Babraham Institute. Bismark's output is designed to be easily interpretable by bench scientists, making it a valuable resource for studying DNA methylation patterns.Bismark is a flexible and efficient tool for analyzing bisulfite sequencing (BS-Seq) data, which captures genome-wide cytosine methylation at single base resolution. It performs both read mapping and methylation calling in a single step, discriminating between CpG, CHG, and CHH contexts. Bismark addresses the computational challenges of bisulfite mapping by running four parallel alignment processes to determine the strand origin of each read. This approach ensures accurate and unbiased methylation analysis, even for partial methylation. The tool is released under the GNU GPLv3+ license and is freely available from the Bioinformatics Group at the Babraham Institute. Bismark's output is designed to be easily interpretable by bench scientists, making it a valuable resource for studying DNA methylation patterns.