Abstract
The development of next-generation sequencing tech-nologies has helped sequence large genomes easily, producing a huge number of short-reads - small frag-ments 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-nucleo-tide polymorphism (SNP) calling between our aligner and BWA - the preferred alignment program. The re-sults showed that the BWA delivers higher recall and F-score, while BWTaligner has better precision in high coveragedepth.
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