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metaSPAdes specifications


Unique identifier OMICS_16413
Name metaSPAdes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Pacific Biosciences, Roche, Oxford Nanopore
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 3.10.1
Stability Stable
Source code URL
Maintained Yes




No version available



  • person_outline Sergey Nurk

metaSPAdes citations


Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations

Front Microbiol
PMCID: 5928236
PMID: 29740420
DOI: 10.3389/fmicb.2018.00792
call_split See protocol

[…] The paired-end reads were quality trimmed using Trimmomatic (ver. 0.36) (), merged with FLASh (ver. 1.2.11) (), and assembled de novo with metaSPAdes (ver. 3.10.1) without read error correction (). Taxonomic classifications were assigned to contigs by searching predicted peptide open reading frames (ORFs) against the peptide SEED and Pha […]


Reproducible protocols for metagenomic analysis of human faecal phageomes

PMCID: 5892011
PMID: 29631623
DOI: 10.1186/s40168-018-0446-z

[…] maximum length of 250 and a sliding window that cuts a read once the average quality in a window size of 4 follows below a Phred score of 30. Reads were then assembled on a per sample basis with the metaSPAdes assembler []. Redundancy between samples was removed by aligning all contigs against each other with BLAST+ v2.2.28. Only the longer contig was kept in the reference set when contigs aligne […]


Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage specific evolution

PMCID: 5955933
PMID: 29581530
DOI: 10.1038/s41396-018-0098-9

[…] 0-bp reads with an average 270-bp insert size (Beijing Genomics Institute, Beijing, China). Illumina reads were trimmed to remove the adapter sequences and low-quality bases, and were assembled using metaSPAdes [] with the following parameters (--only-assembler -k 31,41,51,61,71,81,91,101,111,121). Assembled scaffolds ≥ 2500 bp were binned separately using MetaBAT v0.26.1 [] and MyCC []. Results o […]


Deciphering the Human Virome with Single Virus Genomics and Metagenomics

PMCID: 5869506
PMID: 29509721
DOI: 10.3390/v10030113

[…] 20; trim_qual_type: mean; and trim_qual_window: 20. Genome assembly was performed with SPAdes version 3.6.1 [] by applying the following parameters: --sc, -k 33,55,77,99,127, --careful for vSAGs; and metaspades option with parameters -k 33,55,77,99,127 for saliva viromes. Generated vSAGs contigs were subjected to another round of assembly using the Geneious R8 bioinformatic program [] with stringe […]


Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

Nat Commun
PMCID: 5830445
PMID: 29491419
DOI: 10.1038/s41467-018-03317-6

[…] 0, chastityfilter = True. We then normalized read coverage using BBNorm with options target = 40, mindepth = 2. With this trimmed and normalized dataset, we performed a de novo shotgun assembly using metaSPAdes and default parameters.Using the Hi-C read datasets generated as described above, we trimmed each read to 75 bp to avoid discarding reads sequencing through a Hi-C junction. We mapped each […]


A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils

PMCID: 5824556
PMID: 29471872
DOI: 10.1186/s40168-018-0424-5

[…] q-lite v0.20.4 [] in combination with in-house scripts. We used FLASH v1.2.11 (fast length adjustment of short reads) to align high-quality paired-end reads []. Sequences were de novo assembled using metaSPAdes v3.9.0 [], as recommended []. The quality of each assembled metagenome (n = 17) was assessed using MetaQUAST v4.3 []. To provide taxonomic assignments, all contigs were compared to the enti […]


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