Motivation: New long read sequencers promise to transform sequencing andgenome assembly by producing reads tens of kilobases long. However their higherror rate significantly complicates assembly and requires expensive correctionsteps to layout the reads using standard assembly engines. Results: We present an original and efficient spectral algorithm to layoutthe uncorrected nanopore reads, and its seamless integration into astraightforward overlap/layout/consensus (OLC) assembly scheme. The method isshown to assemble Oxford Nanopore reads from several bacterial genomes intogood quality (~99% identity to the reference) genome-sized contigs, whileyielding more fragmented assemblies from a Sacharomyces cerevisiae referencestrain. Availability and implementation: http://github.com/antrec/spectrassembler Contact: antoine.recanati@inria.fr
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