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Updated: Apr 18, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Dinghua Li1, Chi-Man Liu1, Ruibang Luo1
1HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan.
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 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.
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