- recipe spades
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
- Homepage:
- Documentation:
- License:
GPL / GPL-2.0-only
- Recipe:
- Links:
biotools: spades, usegalaxy-eu: spades, doi: 10.1089/cmb.2012.0021, doi: 10.1101/gr.213959.116, doi: 10.1093/gigascience/giz100, doi: 10.1093/bioinformatics/btz349
SPAdes (St. Petersburg genome assembler) is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. However, it might not be suitable for large genomes projects.
SPAdes works with Ion Torrent, PacBio, Oxford Nanopore, and Illumina paired-end, mate-pairs and single reads.
- package spades¶
- versions:
4.0.0-3
,4.0.0-2
,4.0.0-1
,4.0.0-0
,3.15.5-3
,3.15.5-2
,3.15.5-1
,3.15.5-0
,3.15.4-0
,4.0.0-3
,4.0.0-2
,4.0.0-1
,4.0.0-0
,3.15.5-3
,3.15.5-2
,3.15.5-1
,3.15.5-0
,3.15.4-0
,3.15.3-1
,3.15.3-0
,3.15.2-1
,3.15.2-0
,3.15.0-0
,3.14.1-2
,3.14.1-1
,3.14.1-0
,3.14.0-0
,3.13.2-0
,3.13.1-2
,3.13.1-1
,3.13.1-0
,3.13.0-0
,3.12.0-3
,3.12.0-2
,3.12.0-1
,3.12.0-0
,3.11.1-5
,3.11.1-4
,3.11.1-3
,3.11.1-2
,3.11.1-1
,3.11.1-0
,3.11.0-1
,3.11.0-0
,3.10.1-1
,3.10.1-0
,3.10.0-0
,3.9.1-1
,3.9.1-0
,3.9.0-4
,3.9.0-3
,3.9.0-2
,3.9.0-1
,3.9.0-0
,3.8.1-0
,3.8.0-0
,3.7.0-0
,3.6.2-0
,3.5.0-1
,3.5.0-0
- depends _openmp_mutex:
>=4.5
- depends bzip2:
>=1.0.8,<2.0a0
- depends libgcc-ng:
>=12
- depends libgomp:
- depends libstdcxx-ng:
>=12
- depends libzlib:
>=1.2.13,<2.0a0
- depends python:
>=3.8
- requirements:
- additional platforms:
linux-aarch64
,osx-arm64
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install spades and update with:: mamba update spades
To create a new environment, run:
mamba create --name myenvname spades
with
myenvname
being a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/spades:<tag> (see `spades/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/spades/README.html)