recipe confindr

Detect intra- and inter-species bacterial contamination in NGS reads

Homepage

https://github.com/OLC-Bioinformatics/ConFindr

Documentation

https://OLC-Bioinformatics.github.io/ConFindr/

License

MIT / MIT

Recipe

/confindr/meta.yaml

package confindr

(downloads) docker_confindr

Versions

0.7.0-1, 0.7.0-0, 0.6.0-0, 0.5.1-0, 0.5.0-0, 0.4.8-0, 0.4.7-0, 0.4.6-0, 0.4.5-0, 0.4.4-0, 0.4.3-0, 0.4.2-0, 0.4.1-0, 0.4.0-0, 0.3.4-0, 0.3.3-0, 0.3.2-0

Depends bbmap

>=38

Depends biopython

Depends kma

1.2.0.*

Depends mash

>=2

Depends minimap2

Depends pluggy

0.11.0.*

Depends pysam

>=0.15

Depends pytest

Depends python

>=3

Depends rauth

Depends samtools

>=1.6

Requirements

Installation

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

conda install confindr

and update with:

conda update confindr

or use the docker container:

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

(see confindr/tags for valid values for <tag>)