publication . Article . Other literature type . Preprint . 2016

Fast and accurate de novo genome assembly from long uncorrected reads

Robert Vaser; Ivan Sović; Niranjan Nagarajan; Mile Šikić;
Open Access Croatian
  • Published: 05 Aug 2016
  • Publisher: Cold Spring Harbor Laboratory Press
  • Country: Croatia
Abstract
<jats:p>The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore datasets we show that Racon coupled with Miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.</jats:p><jats...
Subjects
free text keywords: Biology, Computing, Method
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