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bioRxiv · 10.1101/018234

benchNGS : An approach to benchmark short reads alignment tools

Farzana Rahman·Mehedi Hassan·Alona Martin Kryshchenko·Inna Dubchak·Nikolai Nickolai Alexandrov·Tatiana Tatarinova
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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.\n\nWe 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.

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Farzana Rahman, Mehedi Hassan, Alona Martin Kryshchenko, Inna Dubchak, Nikolai Nickolai Alexandrov, Tatiana Tatarinova. 2015-04-18. benchNGS : An approach to benchmark short reads alignment tools. https://doi.org/10.1101/018234

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