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DOI: 10.5445/IR/1000064366

libgapmis: extending short-read alignments

Alachiotis, Nikolaos; Berger, Simon; Flouri, Tomáš; Pissis, Solon P; Stamatakis, Alexandros

Abstract:
Background: A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read–the seed–an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read–extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable.
Results: In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart f ... mehr


Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Jahr 2013
Sprache Englisch
Identifikator ISSN: 1471-2105
URN: urn:nbn:de:swb:90-643664
KITopen ID: 1000064366
Erschienen in BMC bioinformatics
Band 14
Heft Suppl 11
Seiten Art. Nr.: S4
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