A description of a typical workflow with this program can be found on the
manual page.
If the program was useful for you, please cite it in your work.
Webstart
The program r2cat can be executed to run locally on your computer using the
Java WebStart technology. The download size to start the program is approximately 1
MByte.
- If an error is issued during WebStart it is quite likely that your Java
version is too old. The program uses features of Java 1.6 (SE 6).
- If you do not have a Java Runtime Environment version 1.6 or higher
installed, or if you are working on Solaris/Linux and never previously used
Java WebStart, please follow these installation instructions.
- Java WebStartmight complain that it cannot verify the digital signature.
Our certificate is signed by Deutsche Telekom Root CA 2 which has
been added to the trusted certificates since
Java Version 6 Update
11.
- If webstart doesn't work for you, you can alternatively run it locally (see below).
Local Usage
See dowload section for local usage of r2cat.
External matching
If you want to use BLAST for matching you can use the following perl script: blast_to_r2cat.pl In order to work,
the Perl module Bio::SeqIO and BLAST (blastall) have to be installed.
The
script matches the specified contigs on the reference(s) and reformates the matching
result such that it can be loaded within r2cat.
About
r2cat was developed by Peter Husemann, Bielefeld University.
Acknowledgements
Thanks to the FreeHEP
project for the image (vector & bitmap) export code (licensed under LGPL). the
Xerces project for the class XMLCharacterProperties that is necessary for svg output
(licensed under the Apache Software License).
