benchNGS : An approach to benchmark short reads alignment tools

, , , , ,
1 University of South Wales, Treforest, United Kingdom
2 School of Computing and Mathematics, University of South Wales, Pontypridd, Wales, United Kingdom
3 Department of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, United States of America
4 Joint Genome Institute, Walnut Creek, California, United States of America
5 Keck Medical School, Children's Hospital Los Angeles, Los Angeles, United States of America
6 International Rice Research Institute, Los Banos, Philippines
DOI
10.7287/peerj.preprints.1007v1
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
Rahman F, Hassan M, Kryshchenko A, Dubchak I, Tatarinova TV, Alexandrov NN. 2015. benchNGS : An approach to benchmark short reads alignment tools. PeerJ PrePrints 3:e1007v1

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.