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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2018.00035

Comparison of Burrows-Wheeler transform-based mapping algorithms used in high-throughput whole-genome sequencing: application to Illumina data for livestock genomes

  • 1U.S. Meat Animal Research Center (ARS-USDA), United States

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. The mappers were evaluated based on two criteria, computational resource/time requirements and robustness of mapping. Our results show that BWA and Bowtie2 tend to be more robust than HISAT2, while HISAT2 was significantly faster and used less memory than both BWA and Bowtie2. We conclude that there is not a single mapper that is ideal in all scenarios but rather the choice of alignment tool should be driven by the application and sequencing technology.

Keywords: Whole-genome sequencing, Mapping algorithm, mapper comparison, Genomic coverage, livestock genome

Received: 10 Oct 2017; Accepted: 25 Jan 2018.

Edited by:

Peng Xu, Xiamen University, China

Reviewed by:

Gregor Gorjanc, University of Edinburgh, United Kingdom
Chao Bian, Beijing Genomics Institute (BGI), China  

Copyright: © 2018 Keel and Snelling. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Brittney Keel, U.S. Meat Animal Research Center (ARS-USDA), Clay Center, United States, brittney.keel@ars.usda.gov