metaSPAdes: a new versatile metagenomic assembler

metaSPAdes: a new versatile metagenomic assembler

2017 | Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A. Pevzner
The article introduces metaSPAdes, a new metagenomic assembler designed to address the challenges of assembling complex microbial communities. The authors highlight the difficulties in metagenomic assembly, such as low coverage, interspecies repeats, and strain mixtures, and explain how metaSPAdes addresses these issues. MetaSPAdes combines algorithmic ideas from SPAdes, a tool initially developed for single-cell and highly polymorphic diploid genome assemblies, with novel features tailored for metagenomics. The software is benchmarked against other state-of-the-art assemblers (IDBA-UD, Ray-Meta, and MEGAHIT) using both synthetic and real datasets, demonstrating superior performance in terms of scaffold length, gene prediction, and read alignment statistics. The article also discusses the scaling of metaSPAdes for large datasets and provides details on its implementation and availability.The article introduces metaSPAdes, a new metagenomic assembler designed to address the challenges of assembling complex microbial communities. The authors highlight the difficulties in metagenomic assembly, such as low coverage, interspecies repeats, and strain mixtures, and explain how metaSPAdes addresses these issues. MetaSPAdes combines algorithmic ideas from SPAdes, a tool initially developed for single-cell and highly polymorphic diploid genome assemblies, with novel features tailored for metagenomics. The software is benchmarked against other state-of-the-art assemblers (IDBA-UD, Ray-Meta, and MEGAHIT) using both synthetic and real datasets, demonstrating superior performance in terms of scaffold length, gene prediction, and read alignment statistics. The article also discusses the scaling of metaSPAdes for large datasets and provides details on its implementation and availability.
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[slides and audio] metaSPAdes%3A a new versatile metagenomic assembler.