BWTaligner: a genome short-read aligner

Main Article Content

Lam Nguyen Xuan Thi Trinh Hien Trinh Dang Hung Tran Cuong Nguyen


The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genome analysis, still remains a challenge. In this study, we develop a short-read alignment program, BWTaligner, based on the Burrows-Wheeler transform compression - exact and inexact matching. We tested it on the paired-end read data simulated from chromosome 9 of the rice genome to compare the alignment and single-nucleotide polymorphism (SNP) calling between our aligner and BWA - the preferred alignment program. The results showed that the BWA delivers higher recall and F-score, while BWTaligner has better precision in high coverage depth.



Article Details

How to Cite
NGUYEN, Lam et al. BWTaligner: a genome short-read aligner. Vietnam Journal of Science, Technology and Engineering, [S.l.], v. 60, n. 2, p. 73-77, june 2018. ISSN 2525-2461. Available at: <>. Date accessed: 21 july 2019.