recipe aquamis

AQUAMIS is a snakemake pipeline for routine assembly and quality assessment of microbial isolate sequencing experiments.

Homepage:

https://gitlab.com/bfr_bioinformatics/AQUAMIS

License:

BSD-3

Recipe:

/aquamis/meta.yaml

package aquamis

Versions:

1.3.7-0,  1.3.6-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.0-0

Depends:

• biopython >=1.78

• bracken >=2.6.0

• cerberus >=1.3.2

• confindr >=0.7.4

• fastp >=0.20.1

• genson >=1.2.2

• jsonschema >=3.2

• kmc 3.1.0.*

• kraken2 >=2.1.1

• mash >=2.3

• mlst >=2.19.0

• numpy >=1.19

• pandas >=1.2.3

• pandoc 2.11.*

• python >=3.7

• pyyaml >=5.4.1

• quast >=5.0.2

• r-base 3.6.3.*

• r-dt >=0.16

• r-knitr >=1.31

• r-rmarkdown <=2.7

• r-rrapply 1.2.2.*

• r-tidyverse 1.3.0.*

• r-urltools 1.7.3.*

• shovill >=1.1.0

• snakemake-minimal >=6.0.0

• taxonkit >=0.6.2

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install aquamis

and update with:

conda update aquamis

or use the docker container:

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

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

Download stats

Link to this page

Render an badge with the following MarkDown:

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