auto_process_ngs

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.

Overview

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.

Installation

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-links argument to the install command to pull in the dependencies.
• For pip 1.6: you must first do pip install -r requirements.txt to pull in the dependencies.

Documentation

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.

Running Tests

The tests can be run using::

python setup.py test

In addition the tests are run via GitHub Actions whenever the repository is updated:

.. image:: https://github.com/fls-bioinformatics-core/auto_process_ngs/workflows/Python%20CI/badge.svg :target: https://github.com/fls-bioinformatics-core/auto_process_ngs/actions?query=workflow%3A%22Python+CI%22

Dependencies

The package depends on the genomics-bcftbx package, available from https://github.com/fls-bioinformatics-core/genomics

Developmental version

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).