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. 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

Dinghua Li  1 , Chi-Man Liu  1 , Ruibang Luo  1 , Kunihiko Sadakane  1 , Tak-Wah Lam  2
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Free article

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

Dinghua Li et al. Bioinformatics. .
Free article

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.

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