A Spectral Algorithm for Fast de Novo Layout of Uncorrected Long Nanopore Reads

TITLE: A Spectral Algorithm for Fast de Novo Layout of Uncorrected Long Nanopore Reads.

AUTHORS: Antoine Recanati, Thomas Brüls, Alexandre d'Aspremont

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 overlaplayoutconsensus (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 a Sacharomyces cerevisiae reference strain.

STATUS: Submitted.

CODE: Available here

ArXiv PREPRINT: ArXiv 1609.07293

PAPER: A Spectral Algorithm for Fast de Novo Layout of Uncorrected Long Nanopore Reads in pdf.