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Old 07-29-2010, 07:08 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Could you store CSFASTQ instead of CSFASTA and QUAL files? Pre-compression that should save a lot of disk space (in fact, even CSFASTA + CSFASTQ should still take less space than CSFASTA + QUAL).

The reason is simply QUAL needs 2 or 3 bytes per score (separator and one or two digits), while (colour space) FASTQ just needs 1 byte per score.

Assuming you are compressing the files anyway this may not make such a big difference, but it might be worth trying.
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