GapMis-OMP: Pairwise Short-Read Alignment on Multi-core ArchitecturesReport as inadecuate

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1 HITS - Heidelberg Institute for Theoretical Studies 2 School of Mathematics and Statistics, The University of Western Australia 3 Department of Informatics King-s College London 4 School of CSE - School of Computer Science and Engineering Seoul 5 Florida Museum of Natural History

Abstract : Pairwise sequence alignment has received a new motivation due to the advent of next-generation sequencing technologies, particularly so for the application of re-sequencing—the assembly of a genome directed by a reference sequence.
After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality fragment of the read allowing a number of mismatches and the insertion of a single gap in the alignment.
In this article, we present GapMis-OMP, a tool for pairwise short-read alignment that works on multi-core architectures.
It is designed to compute the alignments between all the sequences in a first set of sequences and all those from a second one in parallel.
The presented experimental results demonstrate that GapMis-OMP is more efficient than most popular tools.

Author: Tomáš Flouri - Costas Iliopoulos - Kunsoo Park - Solon Pissis -



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