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A spectral algorithm for fast de novo layout of uncorrected long nanopore reads

Author:
Recanati, Antoine, Brüls, Thomas, d’Aspremont, Alexandre
Source:
Bioinformatics 2017 v.33 no.20 pp. 3188-3194
ISSN:
1460-2059
Subject:
algorithms, bioinformatics, genome, genome assembly, nanopores
Abstract:
New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However, their high error rate significantly complicates assembly and requires expensive correction steps to layout the reads using standard assembly engines. We present an original and efficient spectral algorithm to layout the uncorrected nanopore reads, and its seamless integration into a straightforward overlap/layout/consensus (OLC) assembly scheme. The method is shown to assemble Oxford Nanopore reads from several bacterial genomes into good quality (∼99% identity to the reference) genome-sized contigs, while yielding more fragmented assemblies from the eukaryotic microbe Sacharomyces cerevisiae. https://github.com/antrec/spectrassembler. antoine.recanati@inria.fr Supplementary data are available at Bioinformatics online.
Agid:
6248906