Scripts are organised into the following directories:

• build-indexes: contains scripts for building genome indexes for various programs
• ChIP-seq: contains ChIP-seq-specific scripts
• RNA-seq: contains RNA-seq-specific scripts
• microarray: contains microarray-specific scripts
• NGS-general: contains general NGS scripts not specific to a particular type of experiment
• QC-pipeline: contains scripts for running QC pipelines on SOLiD data sets
• solid2cluster: utilities for copying data from SOLiD instrument to cluster
• illumina2cluster: utilities for transferring and preparing Illumina data on the compute cluster
• utils: non-NGS utility scripts
• share: common libraries and modules shared between applications

• R
• perl Statistics::Descriptive module
• BioPerl
• java
• python (2.4+)
• python xlwt, xlrd, xlutils libraries