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

1.0.2-0,  1.0.1-1,  1.0.1-0,  1.0.0-1,  1.0.0-0

Depends

• ariba >=2.9.1

• biopython >=1.68,<1.78

• 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>)

Download stats

Link to this page

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