Overview
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 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.
Documentation
Installing Dindel
In order to get AutoCSA working we recommend that you run through the Quick Start Guide using the sample data set provided.
Help documents
- Quick Start Guide (PDF to come)
- Installation and User Guide (PDF to come)
- Detailed Description of the Algorithm (PDF to come)
- FAQ (PDF to come)
Demo of AutoCSA web-based viewer
CSA results
Download results as comma-separated values
| Amplimer name | Comparison data | Wildtype panel | Reads with variants |
|---|---|---|---|
| *** Need to discuss how to pull all these across. *** | |||
| BRAFexon11 | Results | Wildtypes | 2 |
| INSRRexon3 | Results | Wildtypes | 2 |
| STK11exon1 | Results | Wildtypes | 2 |
| TNNI3Kexon23 | Results | Wildtypes | 2 |
AutoCSA API
Open AutoCSA API
All of the files required to incorporate AutoCSA into your own pipeline are generated as part of the install process.
- csa.jar
- resources (dir)
The resources directory and contents must be in the directory that the subsequent application is executed from.
Software and libraries
Standalone AutoCSA was developed using Netbeans IDE (v5.5).The installer was created using (v3.10.0). The following java libraries have been used in the development of Standalone AutoCSA.
- Apache Jakarta Commons
- Log4j
- Apache Velocity Engine
-
Netbeans
- swing-layout-1.0.1 (provided by Netbeans 5.5 GUI builder)
Downloads
| File | Version | Description | Released |
|---|---|---|---|
| AutoCSA | 1.0 | Includes example data files | 6/06/07 |
| AutoCSA API | 1.0 | Javadocs | 22/02/07 |
Please read the licensing agreement before downloading and using the software:
CGP Software License
Copyright © 2006 Genome Research Ltd.
Author: Cancer Genome Project, cgpit@sanger.ac.uk
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.
Contact
If you have any problems with installing AutoCSA please contact us at the following address, cgpit@sanger.ac.uk.
