recipe spades

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

Homepage

http://cab.spbu.ru/software/spades/

Documentation

http://cab.spbu.ru/files/release3.14.1/manual.html

Developer docs

https://github.com/ablab/spades

License

GPL / GPLv2

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
3.14.1-03.14.0-03.13.2-03.13.1-23.13.1-13.13.1-03.13.0-03.12.0-13.12.0-0

3.14.1-03.14.0-03.13.2-03.13.1-23.13.1-13.13.1-03.13.0-03.12.0-13.12.0-03.11.1-43.11.1-33.11.1-23.11.1-13.11.1-03.11.0-13.11.0-03.10.1-13.10.1-03.10.0-03.9.1-03.9.0-43.9.0-33.9.0-23.9.0-13.9.0-03.8.1-03.8.0-03.7.0-03.6.2-03.5.0-13.5.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install spades

and update with:

conda update spades

or use the docker container:

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

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