title: deBGA: read alignment with de Bruijn graph-based seed and extension.
abstract: 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.
authors.affiliation: Center for Bioinformatics, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.affiliation: Center for Bioinformatics, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Hongzhe
authors.initials: H
authors.lastname: Guo
authors.affiliation: Department of Computer Science, University of Toronto, ON M5S 3G4, Canada Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Brudno
authors.affiliation: Center for Bioinformatics, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Yadong
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D000818:Animals; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA