Tạp chí Khoa học và Công nghệ Việt Nam, S. 2C (2018)

Cỡ chữ:  Nhỏ  Vừa  Lớn

BWTaligner: A genome short-read aligner.

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

Tóm tắt

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.