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  • BSMAP: whole genome Bisulfite Sequence MAPping program

    Hi folks,

    BSMAP: whole genome Bisulfite Sequence MAPping program
    Background Bisulfite 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. Results We 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. Conclusion BSMAP 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/ .

  • #2
    @Wei: Will your BSMAP support SOLiD data input in the future?

    Best regards
    Axel

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    • #3
      It would be great if you'd create an entry in the software wiki for your program

      Comment


      • #4
        example BSMAP alignment file

        Is any one aware of where I can get an example BSMAP Alignment file??

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        • #5
          If you want the SAM variant (it also has its own output format), just PM me with your email address and I can send you a small example.

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