Introduction

DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools. BatMeth is freely available at http://code.google.com/p/batmeth/.

Publications

  1. BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.
    Cite this
    Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK, 2012-01-01 - Genome biology

Credits

  1. Jing-Quan Lim
    Developer

  2. Chandana Tennakoon
    Developer

  3. Guoliang Li
    Developer

  4. Eleanor Wong
    Developer

  5. Yijun Ruan
    Developer

  6. Chia-Lin Wei
    Developer

  7. Wing-Kin Sung
    Investigator

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Summary
AccessionBT006283
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Submitted ByWing-Kin Sung