calcDiversity VS FASTQC

[netpumber]

Hello folks!

On this manual, Illumina in the post alignement stage talks about a script called calcDiversity that helps to calculate if the library is LOW, MEDIUM or HIGH divergent.

From the other hand many people use the tool FASTQC for the quality control of the results.

Is there any significant difference between those two tools ? Is there any alternative too for such a job ?

Thank you.

[GenoMax]

I have not used the calculatediversity tool from CASAVA but based on the release notes it is counting number of unique fragments in a library. There is no indication of subsampling so perhaps it is looking at all data.

FastQC duplication and over-represented sequences module only looks at first 8000 sequences (and then reads them to the end of the file).

Note: Will try the calculatediversity tool later this morning and see what kind of output it produces.

dedupe.sh from BBMap will also provide an indication of duplication (http://seqanswers.com/forums/showthread.php?t=45909), if that is what you are looking for.