https://github.com/fls-bioinformatics-core/auto_process_ngs
Scripts and utilities for automatic processing & management of Illumina NGS sequencing data within the Bioinformatics Core Facility at the University of Manchester
https://github.com/fls-bioinformatics-core/auto_process_ngs
10xgenomics automation bioinformatics fastq-files illumina next-generation-sequencing pipeline qc sequencing
Last synced: 3 months ago
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Scripts and utilities for automatic processing & management of Illumina NGS sequencing data within the Bioinformatics Core Facility at the University of Manchester
- Host: GitHub
- URL: https://github.com/fls-bioinformatics-core/auto_process_ngs
- Owner: fls-bioinformatics-core
- License: afl-3.0
- Created: 2015-08-14T06:53:01.000Z (over 10 years ago)
- Default Branch: devel
- Last Pushed: 2026-01-16T16:00:50.000Z (3 months ago)
- Last Synced: 2026-01-17T04:07:02.830Z (3 months ago)
- Topics: 10xgenomics, automation, bioinformatics, fastq-files, illumina, next-generation-sequencing, pipeline, qc, sequencing
- Language: Python
- Homepage:
- Size: 9.38 MB
- Stars: 10
- Watchers: 5
- Forks: 6
- Open Issues: 77
-
Metadata Files:
- Readme: README.rst
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
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 https://auto-process-ngs.readthedocs.io.
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 `_
in the pip documentation).
Contributing
************
See `CONTRIBUTING.md `_ file for guidelines on how to
contribute to the project.