deBGA: read alignment with de Bruijn graph-based seed and extension

Motivation: 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.
Results: 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.
Availability and Implementation: deBGA is available at: https://github.com/hitbc/deBGA.
Contact: [e-mail]
Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - October 24, 2016 Category: Bioinformatics Authors: Liu, B., Guo, H., Brudno, M., Wang, Y. Tags: SEQUENCE ANALYSIS Source Type: research