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

TL;DR

This paper introduces a spectral algorithm for rapidly assembling uncorrected long nanopore reads, significantly reducing the need for error correction and enabling efficient genome assembly.

Contribution

The paper presents a novel spectral algorithm that efficiently layouts uncorrected nanopore reads within an OLC assembly framework, improving assembly quality and speed.

Findings

Assembles bacterial genomes into ~99% identity contigs

Produces more fragmented assemblies for yeast genome

Integrates seamlessly into existing assembly pipelines

Abstract

Motivation: 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. Results: 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 a Sacharomyces cerevisiae reference strain. Availability and implementation: http://github.com/antrec/spectrassembler Contact: antoine.recanati@inria.fr