benchNGS : An approach to benchmark short reads alignment tools
- Published
- Accepted
- Subject Areas
- Bioinformatics
- Keywords
- Benchmark, NGS, BLAST, bwa, SHRiMP, SOAP, short reads, alignment, Bowtie
- Copyright
- © 2015 Rahman et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. benchNGS : An approach to benchmark short reads alignment tools. PeerJ PrePrints 3:e1007v1 https://doi.org/10.7287/peerj.preprints.1007v1
Abstract
In the last decade a number of algorithms and associated software were developed to align next generation sequencing (NGS) reads to relevant reference genomes. The results of these programs may vary significantly, especially when the NGS reads are contain mutations not found in the reference genome. Yet there is no standard way to compare these programs and assess their biological relevance. We propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. In this paper we outline the method and also present a short report of an experiment performed on five popular alignment tools .
Author Comment
This is a submission to PeerJ for review.