AutoCSA 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.

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 Sun’s Javasite.

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.


To download AutoCSA, please visit:

Further information

CGP Software License

Copyright © 2006 Genome Research Ltd.
Author: Cancer Genome Project,

This software is provided “as is”, without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software.

This code is free software; you can redistribute it and/or modify it under the terms of the BSD License.

Any redistribution or derivation in whole or in part including any substantial portion of this code must include this copyright and permission notice.