SAGE2: parallel human genome assembly

Michael Molnar; Ehsan Haghshenas; Lucian Ilie

doi:10.1093/bioinformatics/btx648

SAGE2: parallel human genome assembly

Bioinformatics. 2018 Feb 15;34(4):678-680. doi: 10.1093/bioinformatics/btx648.

Authors

Michael Molnar¹, Ehsan Haghshenas², Lucian Ilie¹

Affiliations

¹ Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada.
² School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

PMID: 29045591
DOI: 10.1093/bioinformatics/btx648

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 information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Animals
Genome, Human*
High-Throughput Nucleotide Sequencing / methods*
Humans
Sequence Analysis, DNA / methods*
Software*