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

Versions:

0.7.4-0,  0.7.3-0,  0.7.2-0,  0.7.1-0,  0.7.0-1,  0.7.0-0,  0.6.0-0,  0.5.1-0,  0.5.0-0, 

0.7.4-0,  0.7.3-0,  0.7.2-0,  0.7.1-0,  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

• biopython

• kma 1.2.0.*

• mash >=2

• minimap2

• pluggy 0.11.0.*

• pysam >=0.15

• pytest

• python >=3

• rauth

• samtools >=1.6

Required By:

• aquamis

Installation

With an activated Bioconda channel (see 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>)

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