metaspades

name	metaspades
description	More sensitive metagenomic assembly via SPAdes meta mode. Use this skill when working with metaspades: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/ablab/spades. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["assembly","spades"]
upstream	https://github.com/ablab/spades

metaSPAdes

Upstream: ablab/spades (metaspades.py)

Citation

Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017). https://doi.org/10.1101/gr.213959.116

See also docs/references.md.

Analytical thinking

metaSPAdes often yields longer contigs than MEGAHIT at substantially higher memory/time cost. Use it when continuity of medium/low-abundance genomes matters and hardware allows. Hybrid Illumina+long-read modes exist—record which reads entered assembly vs coverage.

Prerequisites

Requirement	Minimum	Recommended
RAM	100 GB+ typical	500 GB–1 TB large
CPU	16	32+
Input	Dehosted PE (± long)	Clean PE from kneaddata

How to run

metaspades.py -t 32 -m 500 \
  -1 s1_1.fastq -2 s1_2.fastq \
  -o temp/metaspades
# multi-library: repeat -1/-2 pairs per SPAdes docs

Primary contigs usually at temp/metaspades/contigs.fasta.

Decision tree

Assembly priority?
├─ Speed/memory → megahit
├─ Continuity / hybrid short+long → metaspades
└─ Already have good contigs → skip; go to prodigal / metawrap / basalt

Related skills

megahit · prodigal · basalt · compute via setup