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

(downloads) docker_spades

Versions:
4.2.0-2,  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, 

4.2.0-2,  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:

  • on _openmp_mutex >=4.5

  • on bzip2 >=1.0.8,<2.0a0

  • on libgcc >=13

  • on libgomp

  • on libstdcxx >=13

  • on libzlib >=1.3.1,<2.0a0

  • on openmpi >=4.1.6,<5.0a0

  • on python >=3.8

Additional platforms:
linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install spades

to add into an existing workspace instead, run:

pixi add spades

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install spades

Alternatively, to install into a new environment, run:

conda create -n envname spades

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/spades:<tag>

(see spades/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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