Introduction

As high-throughput sequencing (HTS) technology becomes ubiquitous and the volume of data continues to rise, HTS read alignment is becoming increasingly rate-limiting, which keeps pressing the development of novel read alignment approaches. Moreover, promising novel applications of HTS technology require aligning reads to multiple genomes instead of a single reference; however, it is still not viable for the state-of-the-art aligners to align large numbers of reads to multiple genomes.We propose de Bruijn Graph-based Aligner (deBGA), an innovative graph-based seed-and-extension algorithm to align HTS reads to a reference genome that is organized and indexed using a de Bruijn graph. With its well-handling of repeats, deBGA is substantially faster than state-of-the-art approaches while maintaining similar or higher sensitivity and accuracy. This makes it particularly well-suited to handle the rapidly growing volumes of sequencing data. Furthermore, it provides a promising solution for aligning reads to multiple genomes and graph-based references in HTS applications.deBGA is available at: https://github.com/hitbc/deBGA CONTACT: ydwang@hit.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.

Publications

  1. deBGA: read alignment with de Bruijn graph-based seed and extension.
    Cite this
    Liu B, Guo H, Brudno M, Wang Y, 2016-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Bo Liu
    Developer

    Center for Bioinformatics, Harbin Institute of Technology, China

  2. Hongzhe Guo
    Developer

    Center for Bioinformatics, Harbin Institute of Technology, China

  3. Michael Brudno
    Developer

    Department of Computer Science, University of Toronto, Canada

  4. Yadong Wang
    Investigator

    Center for Bioinformatics, Harbin Institute of Technology, China

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Summary
AccessionBT000569
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByYadong Wang