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.
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