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AutoCSA (Automatic Comparative Sequence Analysis) is a mutation detection program designed to detect small mutations (1-50 bases) in sequence traces. The software is capable of detecting both homozygous and heterozygous base substitutions, as well as small insertions and deletions, to a high sensitivity.
It has specifically been written with high throughput environments in mind, so it is easy to automate the analysis of large amounts of data with little manual intervention.
For a quick demo of AutoCSA web-based viewer click here. In order to get AutoCSA working we recommend that you run through the Quick Start Guide using the sample data set provided.
The following documentation is available:-
- Quick Start Guide
- Installation and User Guide
- Detailed Description of the Algorithm
- Using the AutoCSA API
- AutoCSA API
- Software and libraries
- FAQ
If you have any problems with installing autoCSA please contact us at the following address, cgpit@sanger.ac.uk.
AutoCSA is written in java and will run under java 1.4 or later versions which must be downloaded and installed on your computer. It is available from Oracle's Java site.
The software is optimised to run with sequence traces generated by ABI3730 sequencers running with 36cm (short) capillaries, the RapidSeq-15sec run module and POP7 sequencing buffer.
It should be emphasised that AutoCSA uses the raw sequence channels from the trace files generated by the ABI sequencers (.ab1 file extension). Traces which have been processed and the raw channels removed are not suitable for use with the software.
The software has been tested successfully under Linux, MS windows XP, and Mac OS X 10.
Please read the licensing agreement before downloading and using the software.
| File | Version | Description | Released |
|---|---|---|---|
| AutoCSA | 1.0 | Includes example data files | 6/06/07 |
| AutoCSA API | 1.0 | Javadocs | 22/02/07 |