recipe qcumber

Quality control, quality trimming, adapter removal and sequence content check of NGS data.

Homepage

https://gitlab.com/RKIBioinformaticsPipelines/QCumber

License

LGPL3

Recipe

/qcumber/meta.yaml

package qcumber

(downloads) docker_qcumber

Versions

2.0.4-0

Depends bioconductor-savr

Depends bitstring

Depends bowtie2

2.3.*

Depends docopt

Depends fastqc

0.11.*

Depends jinja2

Depends kraken

0.10.*

Depends krona

Depends matplotlib

2.0.*

Depends numpy

Depends pandas

Depends python

3.6.*

Depends pyyaml

3.12.*

Depends r

3.3.*

Depends r-ggplot2

2.2.*

Depends r-quantreg

Depends r-reshape2

Depends r-stringi

Depends samtools

1.3.*

Depends seaborn

Depends setuptools

Depends snakemake

3.12.*

Depends trimmomatic

0.36.*

Depends xmltodict

Requirements

Installation

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

conda install qcumber

and update with:

conda update qcumber

or use the docker container:

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

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