metaSPAdes: a new versatile metagenomic assembler
- 1Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004;
- 2Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia 198515;
- 3Department of Computer Science and Engineering, University of California, San Diego, California 92093-0404, USA
- Corresponding author: sergeynurk{at}gmail.com
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↵4 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.213959.116.
- Received August 1, 2016.
- Accepted March 13, 2017.
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