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

• DOI: 10.1093/bioinformatics/btw371
• Publication Date: 2016-07-05T01:59:34Z
• Authors: Bo Liu; Hongzhe Guo; Michael Brudno; Yadong Wang
• Keywords: De Bruijn graph; Limiting

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 development novel approaches. Moreover, promising applications require aligning reads multiple genomes instead a single reference; however, it still not viable for state-of-the-art aligners align large numbers genomes.We propose de Bruijn Graph-based Aligner (deBGA), an innovative graph-based seed-and-extension algorithm reference genome that organized indexed using graph. With its well-handling repeats, deBGA substantially faster than approaches while maintaining similar or higher sensitivity accuracy. This makes particularly well-suited handle rapidly growing volumes data. Furthermore, provides solution references in applications.deBGA available at: https://github.com/hitbc/deBGA CONTACT: [e-mail] information: Supplementary are at Bioinformatics online.