NGS Scripts

There are several versions of the pipelines. Several are somewhat historical as they expect older fastq files generated by Illumina RTA 1.3-1.7. While the newer ones are design to expect current (ie. anything generated in 2011) HiSeq data were the fastq files were created on RTA 1.8, which encodes the quality values in Sanger format as opposed to the previous Illumina format that needed to be converted to the Sanger fomat most applications expect as default.