Bioscala is a project mainly written in SCALA and SHELL, it's free.
Scala code for bioinformatics
A bioinformatics library made with the Scala Language.
This project is in it's early days with a minimum function to read fasta files and principaly some code to deal with the Velvet Graph File.
Maven >= 2 http://maven.apache.org/
Scala Language >= 2.8 http://www.scala-lang.org/
Use the git SCM software with the command:
git clone git://github.com/lvaruzza/bioscala.git
Git is available in most of the Linux distributions and in the site:
http://git-scm.com/
mvn install
The commands are availiable as shell scripts in bin directory
Example:
./bin/dumpContigs velvet preprocessor/colorspace_input.csfasta contigs