recipe spades

SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.

Homepage:

https://github.com/ablab/spades

Documentation:

https://ablab.github.io/spades

License:

GPL / GPL-2.0-only

Recipe:

/spades/meta.yaml

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:

4.2.0-1,  4.2.0-0,  4.1.0-0,  4.0.0-4,  4.0.0-3,  4.0.0-2,  4.0.0-1,  4.0.0-0,  3.15.5-3, 

4.2.0-1,  4.2.0-0,  4.1.0-0,  4.0.0-4,  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:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends openmpi:

>=4.1.6,<5.0a0

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>``)

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