recipe seroba

SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references.

Homepage

https://github.com/sanger-pathogens/seroba

License

GPL / GPL3.0

Recipe

/seroba/meta.yaml

SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references. You can use SeroBA to download references from (https://github.com/phe-bioinformatics/PneumoCaT) to do identify the capsular type of Streptococcus pneumoniae.

package seroba

Versions

1.0.1-1,  1.0.1-0,  1.0.0-1,  1.0.0-0

Depends

• ariba >=2.9.1

• biopython >=1.68

• bowtie2

• cd-hit

• kmc >=3.0

• mummer

• pyfastaq >=3.14.0

• pymummer >=0.10.2

• pysam >=0.15.3

• python >=3

• pyyaml >=3.12

• setuptools

Required By

Installation

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

conda install seroba

and update with:

conda update seroba

or use the docker container:

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

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

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/seroba/README.html)