recipe panpasco

Pipeline for pangenome mapping and pairwise SNP distance

Homepage

https://gitlab.com/rki_bioinformatics/panpasco

License

MIT

Recipe

/panpasco/meta.yaml

PANPASCO uses linear computational pan-genomes and pairwise SNP distance calculation to improve distance matrix analyses

package panpasco

Versions

1.0.0-0

Depends

• bedtools 2.27.*

• bioconductor-genomicranges

• bwa 0.7.17.*

• flash 1.2.11.*

• gatk 3.8.*

• picard 2.18.*

• python >3

• r-argparse

• r-base >=3.6,<3.7.0a0

• samtools

• seqtk

• snakemake

• tabix

• trimmomatic 0.36.*

Required By

Installation

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

conda install panpasco

and update with:

conda update panpasco

or use the docker container:

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

(see panpasco/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/panpasco/README.html)