Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes.

ABSTRACT: Ongoing developments and cost decreases in next-generation sequencing (NGS) technologies have led to an increase in their application, which has greatly enhanced the fields of genetics and genomics. Mapping sequence reads onto a reference genome is a fundamental step in the analysis of NGS data. Efficient alignment of the reads onto the reference genome with high accuracy is very important because it determines the global quality of downstream analyses. In this study, we evaluate the performance of three Burrows-Wheeler transform-based mappers, BWA, Bowtie2, and HISAT2, in the context of paired-end Illumina whole-genome sequencing of livestock, using simulated sequence data sets with varying sequence read lengths, insert sizes, and levels of genomic coverage, as well as five real data sets

SUBMITTER: Keel BN 

PROVIDER: S-EPMC5834436 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature