Performance enhancements

[a-kroh]

Hi Martin,

You might want to consider de-compressing the fastq files at the beginning and running all files on the uncompressed files - this might speed up the wall time due to avoidance of uncompression at each analysis step (built into each of the programs used). I have read (but not tested this) that FastQC, for example can get a boost of up to 50% and the same should be true for any of the programmes since they all need to uncompress the data internally before processing it.

All the best
Andreas