benchNGS : An approach to benchmark short reads alignment tools

TL;DR

This paper introduces benchNGS, a benchmarking method for evaluating short reads alignment tools using pre-computed global alignments of related genomes, providing a standardized accuracy assessment.

Contribution

It presents a novel benchmark approach based on global genome alignments to evaluate the accuracy of short reads mapping tools.

Findings

Benchmark applied to five popular tools

Experiment used Escherichia coli genomes and related bacteria

Results highlight differences in tool accuracy

Abstract

In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when the NGS reads are quite different from the available reference genome. We propose a benchmark to assess accuracy of short reads mapping based on the pre-computed global alignment of related genome sequences. In this paper we propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. We outline the method and also present a short report of an experiment performed on five popular alignment tools based on the pairwise alignments of Escherichia coli O6 CFT073 genome with genomes of seven other bacteria.