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De Novo Draft Genome Assembly Using Fuzzy K-mers

Authors:
John Healy
Desmond Chambers

Keywords: genome assembly, anchoring, fuzzy k-mers, fuzzy hash maps

Abstract:
Although second generation sequencing technology can be used to rapidly sequence an entire genome, assembly algorithms require a high level of coverage to produce a complete genomic sequence. We describe a fuzzy k-mer approach that is capable of rapidly ordering and orientating low coverage sequence reads with a high level of accuracy. Using this approach, a draft genome of Mycoplasma genitalium, sampled at varying low levels of coverage, was accurately anchored against the genome of Mycoplasma pneumoniae. The anchored reads were assembled into scaffolds with a vastly increased N50 length and an error rate of <1.5%.

Pages: 104 to 109

Copyright: Copyright (c) IARIA, 2011

Publication date: May 22, 2011

Published in: conference

ISSN: 2308-4383

ISBN: 978-1-61208-137-3

Location: Venice/Mestre, Italy

Dates: from May 22, 2011 to May 27, 2011