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

• Published in: Bioinformatics Vol. 31; no. 10; pp. 1674 - 1676
• Main Authors: Li, Dinghua, Liu, Chi-Man, Luo, Ruibang, Sadakane, Kunihiko, Lam, Tak-Wah
• Format: Journal Article
• Language: English
• Published: England 15.05.2015
• Subjects: Algorithms; Assembling; Assembly; Bioinformatics; Graphics processing units; Graphs; High-Throughput Nucleotide Sequencing; Mathematical models; Metagenomics - methods; Partitioning; Software; Soil; Soil (material)
• ISSN: 1367-4803; 1367-4811; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btv033

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.