BWTaligner: a genome short-read aligner


  • Lam Nguyen Vinmec Research Institute of Stem Cell and Gene Technology
  • Xuan Thi Trinh Faculty of Information Technology, Hanoi Open University
  • Hien Trinh Laboratory of Genetic Engineering, Institute of Biotechnology, Vietnam Academy of Science and Technology
  • Dang Hung Tran Hanoi National University of Education
  • Cuong Nguyen* Vinmec Research Institute of Stem Cell and Gene Technology


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.


Burrows-Wheeler transform, high-throughput sequencing, paired-end short reads, sequence alignment


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Received 6 April 2018; accepted 15 May 2018

How to Cite

Lam Nguyen, Xuan Thi Trinh, Hien Trinh, Dang Hung Tran, & Cuong Nguyen. (2018). BWTaligner: a genome short-read aligner. Vietnam Journal of Science, Technology and Engineering, 60(2), 73-77.



Life Sciences