Introduction

As the next-generation sequencing (NGS) technologies producing hundreds of millions of reads every day, a tremendous computational challenge is to map NGS reads to a given reference genome efficiently. However, existing methods of all-mappers, which aim at finding all mapping locations of each read, are very time consuming. The majority of existing all-mappers consist of 2 main parts, filtration and verification. This work significantly reduces verification time, which is the dominant part of the running time.An efficient all-mapper, BitMapper, is developed based on a new vectorized bit-vector algorithm, which simultaneously calculates the edit distance of one read to multiple locations in a given reference genome. Experimental results on both simulated and real data sets show that BitMapper is from several times to an order of magnitude faster than the current state-of-the-art all-mappers, while achieving higher sensitivity, i.e., better quality solutions.We present BitMapper, which is designed to return all mapping locations of raw reads containing indels as well as mismatches. BitMapper is implemented in C under a GPL license. Binaries are freely available at http://home.ustc.edu.cn/%7Echhy.

Publications

  1. BitMapper: an efficient all-mapper based on bit-vector computing.
    Cite this
    Cheng H, Jiang H, Yang J, Xu Y, Shang Y, 2015-06-01 - BMC Bioinformatics

Credits

  1. Haoyu Cheng
    Developer

    School of Computer Science, University of Science and Technology of China

  2. Huaipan Jiang
    Developer

    School of Computer Science, University of Science and Technology of China

  3. Jiaoyun Yang
    Developer

    Hefei University of Technology, Hefei

  4. Yun Xu
    Developer

    School of Computer Science, University of Science and Technology of China

  5. Yi Shang
    Investigator

    Department of Computer Science, University of Missouri-Columbia

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Summary
AccessionBT002535
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByYi Shang