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Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15.

metaSPAdes: a new versatile metagenomic assembler.

Author information

1
Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004.
2
Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia 198515.
3
Department of Computer Science and Engineering, University of California, San Diego, California 92093-0404, USA.

Abstract

While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.

PMID:
28298430
PMCID:
PMC5411777
DOI:
10.1101/gr.213959.116
[Indexed for MEDLINE]
Free PMC Article

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