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Fast and accurate de novo genome assembly from long uncorrected reads

Vaser, Robert; Sović, Ivan; Nagarajan, Niranjan; Šikić, Mile (2017) Fast and accurate de novo genome assembly from long uncorrected reads. Genome Research, - (-). ---. ISSN 1088-9051

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Abstract

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.

Item Type: Article
Uncontrolled Keywords: genome; high quality assemblies; Racon module
Subjects: NATURAL SCIENCES > Biology
TECHNICAL SCIENCES > Computing
Divisions: Center for Informatics and Computing
Depositing User: Ivan Sović
Date Deposited: 03 Mar 2017 14:08
Last Modified: 03 Mar 2017 14:08
URI: http://fulir.irb.hr/id/eprint/3411
DOI: 10.1101/gr.214270.116

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