SAGE2: Parallel human genome assembly

Abstract

Summary De novo genome assembly of next-generation sequencing data is a fundamental problem in bioinformatics. There are many programs that assemble small genomes, but very few can assemble whole human genomes. We present a new algorithm for parallel overlap graph construction, which is capable of assembling human genomes and improves upon the current state-of-the-art in genome assembly. Availability and implementation SAGE2 is written in C ++ and OpenMP and is freely available (under the GPL 3.0 license) at github.com/lucian-ilie/SAGE2. Contact ilie@uwo.ca Supplementary informationSupplementary dataare available at Bioinformatics online.