Utilities for NGS and genomics-related bioinformatics developed within the Bioinformatics Core Facility (BCF) within the Faculty of Life Sciences (FLS) at the University of Manchester (UoM).
Full documentation is available at http://genomics-bcftbx.readthedocs.org.
The utilities are divided into broad categories:
- Handling data from SOLiD and Illumina sequencers (
- Performing QC and manipulation of NGS data (
- Setting up reference data (
- Supporting analysis of ChIP-seq, RNA-seq and microarray data (
- General non-bioinformatics utilities (
There is also a Python package called
bcftbx which is used by many of the
programs, and which provides a wide range of utility functions.
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
To install directly from github using
pip install git+https://github.com/fls-bioinformatics-core/genomics.git
Many of the scripts should run directly after installation without additional
setup. The exceptions are the QC scripts, which require a
file to be created and edited to point to the locations of the
Documentation based on
sphinx is available under the
To build do either:
python setup.py sphinx_build
cd docs make html
both of which create the documentation in the
The Python unit tests can be run using:
python setup.py test
Note that this requires the
There are also some test scripts in the
these can be run individually or via a 'runner' script:
(Note that this requires that the QC scripts have already been setup after installing the package.)
In addition the tests are run via TravisCI whenever this GitHub repository is updated:
The developmental branch of the code on github is
devel, this can be
pip install git+https://github.com/fls-bioinformatics-core/genomics.git@devel
-e option to install an 'editable' version (see the section on
in the pip documentation),
The tests are run on TravisCI whenever the developmental version is updated:
The package consists predominantly of code written in Python, which has been used extensively with Python 2.6 and 2.7.
In addition there are scripts requiring:
The following packages are required for subsets of the code:
Some of the scripts also use third party software, including:
There are also a couple of Java-based programs.