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

(downloads) docker_seroba

Versions

1.0.1-0, 1.0.0-1, 1.0.0-0

Depends ariba

>=2.9.1

Depends biopython

>=1.68

Depends bowtie2

Depends cd-hit

Depends kmc

>=3.0

Depends mummer

Depends pyfastaq

>=3.14.0

Depends pymummer

>=0.10.2

Depends python

>=3

Depends pyyaml

>=3.12

Depends setuptools

Requirements

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 install-with-bioconda 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)