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

Dinghua Li; Chi-Man Liu; Ruibang Luo; Kunihiko Sadakane; Tak‐Wah Lam · Bioinformatics · 2015

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Author / responsible party
Dinghua Li; Chi-Man Liu; Ruibang Luo; Kunihiko Sadakane; Tak‐Wah Lam
Publisher
Bioinformatics
Year
2015
Language
English

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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: rb@l3-bioinfo.com or twlam@cs.hku.hk Supplementary information: Supplementary data are available at Bioinformatics online.

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APA 7

Li, D, Liu, C. M, Luo, R, Sadakane, K, & Lam, T. (2015). MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. https://doi.org/10.1093/bioinformatics/btv033

MLA

Li, Dinghua, et al. "MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph." 2015. https://doi.org/10.1093/bioinformatics/btv033.

Chicago

Li, Dinghua, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, and Tak‐Wah Lam. 2015. "MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.". https://doi.org/10.1093/bioinformatics/btv033.

Harvard

Li, D. et al. 2015, MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics, available at: https://doi.org/10.1093/bioinformatics/btv033 [Accessed 7 Aug. 2026].

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Title
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct <i>de Bruijn</i> graph
Author / contributors
Dinghua Li; Chi-Man Liu; Ruibang Luo; Kunihiko Sadakane; Tak‐Wah Lam
Publisher
Bioinformatics
Publication year
2015
Language
English

Subjects

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Contig; Metagenomics; De Bruijn graph; Sequence assembly; Computer science; De Bruijn sequence; Software; k-mer; Graphics; Graph; Node (physics); Normalization (sociology)
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