Scripts and utilities for automatic processing & management of NGS sequencing data from Illumina sequencers, developed within the Bioinformatics Core Facility (BCF) at the University of Manchester (UoM).
Full documentation is available at http://auto_process_ngs.readthedocs.org.
This package provides a small set of utilities to generate FASTQ files from
raw bcl files output by Illumina MiSEQ and HiSEQ sequencers, and to
perform other task such as QC runs and file management.
It also facilitates handling problem situations such as barcoding issues or incomplete runs.
It is recommended to use:
pip install .
from within the top-level source directory to install the package.
To use the package without installing it first you will need to add the
directory to your PYTHONPATH environment.
To install directly from github using pip:
pip install git+https://github.com/fls-bioinformatics-core/auto_process_ngs.git
Note
- For pip 1.5: you will need to specify the
--process-dependency-linksargument to theinstallcommand to pull in the dependencies. - For pip 1.6: you must first do
pip install -r requirements.txtto pull in the dependencies.
Documentation based on sphinx is available under the docs directory.
To build:
cd docs make html
which creates the documentation in the docs/build subdirectory.
The tests can be run using:
python setup.py test
In addition the tests are run via GitHub Actions whenever the repository is updated:
The package depends on the genomics-bcftbx package, available from
https://github.com/fls-bioinformatics-core/genomics
The developmental branch of the code on github is devel, this can be
installed using:
pip install git+https://github.com/fls-bioinformatics-core/auto_process_ngs.git@devel
Use the -e option to install an 'editable' version (see the section on
"Editable" installs
<https://pip.pypa.io/en/latest/reference/pip_install.html#editable-installs>_
in the pip documentation).