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Genome Res. 2017 May;27(5):737-746. doi: 10.1101/gr.214270.116. Epub 2017 Jan 18.

Fast and accurate de novo genome assembly from long uncorrected reads.

Author information

1
Department of Electronic Systems and Information Processing, University of Zagreb, Faculty of Electrical Engineering and Computing, 10000 Zagreb, Croatia.
2
Centre for Informatics and Computing, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
3
Genome Institute of Singapore, Singapore 138672, Singapore.
4
Bioinformatics Institute, Singapore 138671, Singapore.

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 that 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 data sets, 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.

PMID:
28100585
PMCID:
PMC5411768
DOI:
10.1101/gr.214270.116
[Indexed for MEDLINE]
Free PMC Article

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