recipe plasmidid

Pipeline for plasmid identification and reconstruction

Homepage

https://github.com/BU-ISCIII/plasmidID

License

GPLv3

Recipe

/plasmidid/meta.yaml

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

package plasmidid

Versions

1.6.5-0,  1.6.4-3,  1.6.4-2,  1.6.4-1,  1.6.4-0,  1.6.3-2,  1.6.3-1,  1.6.3-0,  1.6.2-0, 

1.6.5-0,  1.6.4-3,  1.6.4-2,  1.6.4-1,  1.6.4-0,  1.6.3-2,  1.6.3-1,  1.6.3-0,  1.6.2-0,  1.6.0-0,  1.5.2-0

Depends

• bc

• bedtools

• biopython

• blast

• bowtie2

• circos

• gawk

• mash >=2

• numpy

• pandas

• perl-gd >=2.71

• prokka >=1.14

• python >=3.6

• samtools

• scikit-learn

• scipy

• spades

• tabulate

• tbb 2020.2

• trimmomatic

• wget

Required By

Installation

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

conda install plasmidid

and update with:

conda update plasmidid

or use the docker container:

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

(see plasmidid/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/plasmidid/README.html)