MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
2014/09/25 by Dinghua Li, Li, Dinghua, Chi-Man Liu +7 · 89 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #FOS: Biological sciences #Gene expression and cancer classification #Genomics (q-bio.GN) #Genomics and Phylogenetic Studies #Microbial Community Ecology and Physiology
paper · pdf · doi:10.48550/arxiv.1409.7208
openalex publication_date 2014/09/25 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., it avoids pre-processing like partitioning and normalization, which might compromise on result integrity. MEGAHIT generates 3 times larger assembly, with longer contig N50 and average contig length than the previous assembly. 55.8% of the reads were aligned to the assembly, which is 4 times higher than the previous. The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license.
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