BSMAP: whole genome bisulfite sequence MAPping program

By Yuanxin Xi, Wei Li. BMC Bioinformatics, 2009

1,156 citations recorded by the source corpus.

BackgroundBisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation.ResultsWe developed an efficient bisulfite reads mapping algorithm BSMAP to address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite mapping approaches, BSMAP is faster, more sensitive and more flexible.ConclusionBSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/87445616fb97dadcde62abe80389a33dc6796e04

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Citations in the corpus

Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder (2016, methodology): “74 (37) is used to align clean reads to reference mouse genome mm10.”
A survey of sequence alignment algorithms for next-generation sequencing (2010, background): “Most aligners capable of bisulfite alignments [24, 57] do the following.”
Dnmt3a is essential for hematopoietic stem cell differentiation (2011, methodology): “, the RRBS reads were mapped to the mouse genome (mm9) using RRBSMA”
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules (2012, methodology): “For single-end IMR90 libraries, MAQ (Li et al. 2008) was used with the ‘‘-c’’ bisulfite mode (as in Berman et al. 2012), and for paired-end GBM libraries, BSMAP (Xi and Li 2009) was used.”
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data (2013, methodology): “Other BS aligners, such as BSMAP [10], RMAPBS [11] and GSNAP [12], employ wild-card approaches.”
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions (2012, methodology): “VerJinxer [5] and BSMAP [9], for example, build a ‘seed’ index of the reference genome.”
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling (2011, methodology): “uk/projects/bismark/ ) works in the same way as BS Seeker, but provides additional scripts for producing more convenient DNA methylation data files as output; and (iv) BSMA”
The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers (2010, methodology): “Reads were mapped using BSMAP-1.0240 with minor modifications”