12860

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

Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam
HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong
arXiv:1409.7208 [q-bio.GN], (25 Sep 2014)

@article{2014arXiv1409.7208L,

   author={Li}, D. and {Liu}, C.-M. and {Luo}, R. and {Sadakane}, K. and {Lam}, T.-W.},

   title={"{MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph}"},

   journal={ArXiv e-prints},

   archivePrefix={"arXiv"},

   eprint={1409.7208},

   primaryClass={"q-bio.GN"},

   keywords={Quantitative Biology – Genomics},

   year={2014},

   month={sep},

   adsurl={http://adsabs.harvard.edu/abs/2014arXiv1409.7208L},

   adsnote={Provided by the SAO/NASA Astrophysics Data System}

}

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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 under GPLv3 license.
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