Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1
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. Eff...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2018-02-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fgene.2018.00035/full |
| _version_ | 1828804694015737856 |
|---|---|
| author | Brittney N. Keel Warren M. Snelling |
| author_facet | Brittney N. Keel Warren M. Snelling |
| author_sort | Brittney N. Keel |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T07:44:14Z |
| format | Article |
| id | doaj.art-e434415297e14de4aed919cf2514f377 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T07:44:14Z |
| publishDate | 2018-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-e434415297e14de4aed919cf2514f3772022-12-22T00:32:41ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-02-01910.3389/fgene.2018.00035319058Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1Brittney N. KeelWarren M. SnellingOngoing 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.http://journal.frontiersin.org/article/10.3389/fgene.2018.00035/fullwhole-genome sequencingmapping algorithmmapper comparisongenomic coveragelivestock |
| spellingShingle | Brittney N. Keel Warren M. Snelling Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1 Frontiers in Genetics whole-genome sequencing mapping algorithm mapper comparison genomic coverage livestock |
| title | Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1 |
| title_full | Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1 |
| title_fullStr | Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1 |
| title_full_unstemmed | Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1 |
| title_short | Comparison of Burrows-Wheeler Transform-Based Mapping Algorithms Used in High-Throughput Whole-Genome Sequencing: Application to Illumina Data for Livestock Genomes1 |
| title_sort | comparison of burrows wheeler transform based mapping algorithms used in high throughput whole genome sequencing application to illumina data for livestock genomes1 |
| topic | whole-genome sequencing mapping algorithm mapper comparison genomic coverage livestock |
| url | http://journal.frontiersin.org/article/10.3389/fgene.2018.00035/full |
| work_keys_str_mv | AT brittneynkeel comparisonofburrowswheelertransformbasedmappingalgorithmsusedinhighthroughputwholegenomesequencingapplicationtoilluminadataforlivestockgenomes1 AT warrenmsnelling comparisonofburrowswheelertransformbasedmappingalgorithmsusedinhighthroughputwholegenomesequencingapplicationtoilluminadataforlivestockgenomes1 |