Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1
2018
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.
Mappingsequence reads onto a
reference genomeis a fundamental step in the analysis of NGS
data.
Efficientalignment of the reads onto the
reference genomewith 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 sequencingof 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.
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