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

Bioinformatics (Oxford, England) - Tập 31 Số 10 - Trang 1674-1676 - 2015
Dinghua Li1, Chi-Man Liu1, Ruibang Luo1, Kunihiko Sadakane1, Tak‐Wah Lam1
11 HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, 2L3 Bioinformatics Limited, Hong Kong and 3National Institute of Informatics, Chiyoda-ku, Tokyo, Japan

Tóm tắt

Abstract Summary: 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. Availability and implementation: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license. Contact:  [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

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Tài liệu tham khảo

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Thông tin xuất bản

Bioinformatics (Oxford, England)

Tập 31 Số 10

1674-1676

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