title: MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
abstract: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a fourfold improvement.
authors.affiliation: HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan.
authors.forename: Dinghua
authors.initials: D
authors.lastname: Li
authors.affiliation: HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan.
authors.forename: Chi-Man
authors.initials: CM
authors.lastname: Liu
authors.affiliation: HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan.
authors.forename: Ruibang
authors.initials: R
authors.lastname: Luo
authors.affiliation: HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan.
authors.forename: Kunihiko
authors.initials: K
authors.lastname: Sadakane
authors.affiliation: HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan.
authors.forename: Tak-Wah
authors.initials: TW
authors.lastname: Lam
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods*; D012984:Software; D012987:Soil
chemical_list: D012987:Soil