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.
Cite
@article{arxiv.1409.7208,
title = {MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph},
author = {Dinghua Li and Chi-Man Liu and Ruibang Luo and Kunihiko Sadakane and Tak-Wah Lam},
journal= {arXiv preprint arXiv:1409.7208},
year = {2014}
}
Comments
2 pages, 2 tables, 1 figure, submitted to Oxford Bioinformatics as an Application Note