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Source: qcumber
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all,
python3-setuptools,
fastqc,
trimmomatic,
bowtie2,
kraken,
texlive-latex-base
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/qcumber
Vcs-Git: https://salsa.debian.org/med-team/qcumber.git
Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber
Package: qcumber
Architecture: all
Depends: ${python3:Depends},
${misc:Depends},
python3-jinja2,
python3-matplotlib,
python3-biopython,
libjs-angularjs,
libjs-bootstrap,
libjs-d3,
libjs-jquery,
r-base-core,
r-bioc-savr,
r-cran-ggplot2,
r-cran-quantreg,
snakemake
Recommends: dwgsim,
kraken
Conflicts: qc-pipeline
Provides: qc-pipeline
Replaces: qc-pipeline
Description: quality control of genomic sequences
QCPipeline is a tool for quality control. The workflow is as follows:
.
1. Quality control with FastQC
2. Trim Reads with Trimmomatic
3. Quality control of trimmed reads with FastQC
4. Map reads against reference using bowtie2
5. Classify reads with Kraken
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