- recipe seroba
SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references.
GPL / GPL3.0
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¶
- depends ariba:
- depends bcftools:
- depends biopython:
- depends bowtie2:
- depends cd-hit:
- depends kmc:
- depends mummer:
- depends pyfastaq:
- depends pymummer:
- depends pysam:
- depends python:
- depends pyyaml:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install seroba and update with:: mamba update seroba
To create a new environment, run:
mamba create --name myenvname seroba
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/seroba:<tag> (see `seroba/tags`_ for valid values for ``<tag>``)