recipe pathogen-profiler

Library giving access to classes and functions to create a profiling tool to look for mutations from NGS data.

Homepage:

https://github.com/jodyphelan/pathogen-profiler

License:

GPL3

Recipe:

/pathogen-profiler/meta.yaml

package pathogen-profiler

Versions:

2.0.4-1,  2.0.4-0,  2.0.3-0,  2.0.2-1,  2.0.2-0,  2.0.1-0,  2.0.0-1,  2.0.0-0,  1.7.3-1, 

2.0.4-1,  2.0.4-0,  2.0.3-0,  2.0.2-1,  2.0.2-0,  2.0.1-0,  2.0.0-1,  2.0.0-0,  1.7.3-1,  1.7.3-0,  1.7.2-0,  1.7.1-1,  1.7.1-0,  1.7-0,  1.6.1-0,  1.6-0,  1.5-0,  1.3-0,  1.2-0,  1.1-2,  1.1-1,  1.1-0,  1.0-0,  0.1-3,  0.1-2,  0.1-1,  0.1-0

Depends:

• bcftools >=1.10

• bedtools

• bwa

• cryptography >=39.0.1

• delly 0.8.7.*

• dsk >=2.2

• freebayes >=1.3.5

• gatk4

• git

• kmc >=3.2.1

• lofreq >=2.1.5

• minimap2

• openjdk >=11.0.8

• parallel

• pilon >=1.24

• python >=3.7

• requests

• samclip

• samtools >=1.10

• snpeff >=5.1

• tqdm

• trimmomatic

Required By:

• ntm-profiler

• tb-profiler

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install pathogen-profiler

and update with:

conda update pathogen-profiler

or use the docker container:

docker pull quay.io/biocontainers/pathogen-profiler:<tag>

(see pathogen-profiler/tags for valid values for <tag>)

Download stats

Link to this page

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