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Bioinformatics. 2015 May 15;31(10):1674-6. doi: 10.1093/bioinformatics/btv033. Epub 2015 Jan 20.

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

Author information

1
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.
2
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.

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.

PMID:
25609793
DOI:
10.1093/bioinformatics/btv033
[Indexed for MEDLINE]

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