Abstract
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.
Keywords
ContigMetagenomicsDe Bruijn graphSequence assemblyComputer scienceDe Bruijn sequenceSoftwarek-merGraphicsGraphNode (physics)Normalization (sociology)Graphics processing unitParallel computingComputational biologyTheoretical computer scienceBiologyDNA sequencingComputer graphics (images)MathematicsOperating systemCombinatoricsGenomeEngineeringGenetics
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Publication Info
- Year
- 2015
- Type
- article
- Volume
- 31
- Issue
- 10
- Pages
- 1674-1676
- Citations
- 8475
- Access
- Closed
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Cite This
Dinghua Li,
Chi-Man Liu,
Ruibang Luo
et al.
(2015).
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct <i>de Bruijn</i> graph.
Bioinformatics
, 31
(10)
, 1674-1676.
https://doi.org/10.1093/bioinformatics/btv033
Identifiers
- DOI
- 10.1093/bioinformatics/btv033