Skip to content


Subversion checkout URL

You can clone with
Download ZIP
Scripts, utilities and programs for genomic bioinformatics.
Python Shell Perl Java R
Branch: master
Failed to load latest commit information.
ChIP-seq Update Python programs to accommodate restructuring of library modules.
NGS-general Update READMEs for NGS-general and utils.
QC-pipeline QC-pipeline/test: add a test script runner ''.
RNA-seq RNA-seq/ 1.1.6: fix import of simple_xls from …
bcftbx Merge branch 'devel' into devel-merge
build-indexes Updates to various scripts to properly locate shell function 'librari…
config Move qc.setup.sample to 'config' dir; first round of updating QC scri…
docs docs: more updates to the sphinx documentation.
illumina2cluster Update Python programs to accommodate restructuring of library modules.
microarray Moved from 'utils' to 'microarray'.
share Move qc.setup.sample to 'config' dir; first round of updating QC scri…
solid2cluster Updates to various scripts to properly locate shell function 'librari…
utils Update READMEs for NGS-general and utils.
.gitignore Update .gitignore to ignore outputs from
ChangeLog Update the change log.
LICENSE Added license document.
README.rst Add link to ReadTheDocs in README.
setup.cfg setup.cfg: enables the 'python build_sphinx' command. Move qc_boxplotter from 'NGS-general' to 'QC-pipeline'.



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


The utilities are divided into broad categories:

  • Handling data from SOLiD and Illumina sequencers (solid2cluster, illumina2cluster)
  • Performing QC and manipulation of NGS data (QC-pipeline)
  • Setting up reference data (build-indexes)
  • Supporting analysis of ChIP-seq, RNA-seq and microarray data (ChIP-seq, RNA-seq, microarray, NGS-general)
  • General non-bioinformatics utilities (utils)

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 PYTHONPATH environment.

To install directly from github using pip:

pip install 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 fastq_screen configuration files.


Documentation based on sphinx is available under the docs directory.

To build do either:

python sphinx_build


cd docs
make html

both of which create the documentation in the docs/build subdirectory.

Running Tests

The Python unit tests can be run using:

python test

Note that this requires the nose package.

There are also some test scripts in the QC-pipeline/tests directory, 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.)

Developmental version

The developmental branch of the code on github is devel, this can be installed using:

pip install git+

Use the -e option to install an 'editable' version (see the section on "Editable" installs <>_ in the pip documentation),


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:

  • bash
  • Perl
  • R

The following packages are required for subsets of the code:

  • perl: Statistics::Descriptive and BioPerl
  • python: xlwt, xlrd and xlutils

Some of the scripts also use third party software, including:

  • bowtie
  • bowtie2
  • bfast
  • fastq_screen
  • fastqc
  • convert (from ImageMagick)

There are also a couple of Java-based programs.

Something went wrong with that request. Please try again.