Download Babraham Bioinformatics Projects
All Babraham Bioinformatics code is released under the GNU General public license. You should be aware that some of the downloads on this page include code from other projects which is available under different license terms.
All Babraham Bioinformatics projects are distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
If you have any problems with any of the software you downloaded from here then please report them to us and we'll do our best to get them sorted out.
If you want to stay up to date with changes to our existing projects, or with new software we have released then you can follow us on twitter You can also see demonstrations of our software on our YouTube channel 1
ASAP Performing allele-specific alignments in Next-Gen Sequencing samples with mixed genetic background
Bareback A tool to shuffle low complexity sequence to the end of Illumina sequencing runs
- README
- Bareback_v1.0.tar.gz (includes back-shuffling script)
Bismark A bisulfite read mapper and methylation caller
- Release Notes
- Bismark User Guide v0.21.0
- Bismark test dataset
- Bismark v0.22.3.tar.gz (includes bismark2summary, deduplicate_bismark, bismark2bedGraph, coverage2cytosine and other source code)
- RRBS Guide (PDF, last updated 25 Jan 2017)
ChIPMonk ChIP-on-Chip analysis tool
- README
- Release Notes Please read these if you are upgrading from an older version!!
- ChIPMonk v1.2.3 (Win/Linux zip file)
- ChIPMonk v1.2.3 (Mac DMG image)
- Source Code for ChIPMonk v1.2.3 (zip file)
- Example data file [85MB] (unzip before use) Original paper
Cluster Flow Command line tool for bioinformatics pipelines on a cluster
- Cluster Flow Website (documentation)
- Installation / Usage Tutorial How to set up and run Cluster Flow
- Writing Pipelines and Modules How to write your own Cluster Flow pipelines and modules
- Download Cluster Flow (GitHub releases page)
Compter Analysis and visualisation of sequence composition
Difference Tracker A particle tracker for faint moving particles
- README
- Release Notes Please read these before using the program.
- Difference Tracker v0.1 (Cross Platform jar file)
- Difference Tracker v0.1 source code
FastQC A quality control application for high throughput sequence data
- README
- Installation and setup instructions
- Release Notes Please read these before using the program.
- FastQC v0.12.1 (Win/Linux zip file)
- FastQC v0.12.1 (Mac DMG image)
- Source Code for the latest FastQC release
FastQ Screen A screening application for high througput sequence data
FocalPoint Image Viewer
- README
- CHANGELOG
- KNOWN_PROBLEMS
- FocalPoint v0.6 (Win/Linux zip file)
- FocalPoint v0.6 (Mac DMG image)
- Source Code for FocalPoint v0.6 (zip file)
FRETSaw FRET Image Viewer
- README
- FRETSaw v1.0 (Win/Linux zip file)
- FRETSaw v1.0 (Gzipped Mac DMG image)
- Source Code for FRETSaw v1.0 (zip file)
HiCUP Pipeline for analysing Hi-C data
Labrador Tool for managing and automating the processing of publicly available datasets
- Documentation
- README Please read these before using the program
- Installation Walkthrough Screencast of installing Apache, PHP, MySQL and Labrador on a blank server.
- End-User Usage Tutorial Screencast showing basic usage of Labrador by end-users (not administrators)
- Administration Tutorial Screencast showing basic usage of Labrador by administrators
- Labrador Releases GitHub page
mzViewer mzData Viewer
Realyser Real Time PCR Normalisation tool
re-DOT-able Dot Plot Tool
- Release Notes Please read these before using the program.
- reDOTable v1.2 (Win/Linux zip file)
- reDOTable v1.1 (Mac DMG image)
- Source Code for re-DOT-able from GitHub
reStrainingOrder Mouse Strain/Hybrid Identification
SeqMonk Mapped Sequence Analysis Tool
- README
- INSTALL Installation instructions for the program.
- Release Notes Please read these before using the program.
- SeqMonk v1.48.1 for 64-bit Windows
- SeqMonk v1.48.1 for 64-bit Linux
- SeqMonk v1.48.1 for 64-bit Mac OSX
- Source Code for SeqMonk from GitHub
- Example SeqMonk project - so you can try SeqMonk out easily (216MB)
Sherman bisulfite-treated Read FastQ Simulator
- Sherman Manual (on Github)
- Release Notes (on Github)
- Sherman v0.1.8 (zip file)
Sierra A simple LIMS for sequencing facilities
SNPsplit Allele-specific alignment sorting for N-masked genomes
- SNPsplit User Guide v0.3.2 (pdf; updated 29 March 2017)
- SNPsplit_v0.3.2.tar.gz
- Release Notes
SparkSpotter ImageJ plugin to identify 'Spark' events
- README
- SparkSpotter v1.1 (Pre-configured Jar File)
- SparkSpotter v1.1 Source Code (Cross Platform Zip file)
StackMeasure ImageJ Plugin to identify and measure feautres in images
Trim Galore Consistent quality and adapter trimming for RRBS or standard FastQ files
- Trim Galore User Guide v0.6.1 (Markdown)
- Trim_Galore (hosted at Github) (This includes a brief RRBS Guide; last update: 13 November 2017)