180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.

1. Download the latest USeq_xxx.zip release
2. Uncompress
3. Execute an app with no parameters to pull the help menu, e.g. java -jar USeq_9.1.3/Apps/BamConcordance
4. See the usage and application guides in the USeq_xxxx/Documentation release

1. Clone the github repo.
2. Download Apache ANT libraries (apache-ant-1.9.6-bin.tar.gz) from http://ant.apache.org/bindownload.cgi and unzip.
3. Set ANT_HOME in your bash profile to point to the unzipped ANT directory. Don't forget to source the file to implement the changes.
4. Download the ant-contrib-0.6 (ant-contrib-0.6-bin.zip) from http://sourceforge.net/projects/ant-contrib/files/ant-contrib/. Unzip and move the lib/ant-contrib-0.6.jar to $ANT_HOME/lib directory.
5. In Eclipse, set the Ant HOME: Window > Preferences > Ant Home … > $ANT_HOME
6. Refresh the project in Eclipse.

To install USeq into the Releases/ subfolder:

Right click on the "build.xml" > “Run as … “ > 1 Ant Build.

This will create an unzipped and zipped archive.