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.


metaSPAdes is publicly available as a part of SPAdes package.


In case of any questions, suggestions, bug reports, please write to .


  1. Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ, Sakharova E, Scheremetjew M, Korobeynikov A, Shlemov A, Kunyavskaya O, Lapidus A and Finn RD. MGnify: the microbiome analysis resource in 2020 Nucleic Acids Research, 2020
  2. Nurk S. Assembly of metagenomic (series) data with SPAdes instruments (talk), 2017