automated pipeline casava or FASTQ script/program

sdj · 01-11-2012, 12:52 PM

Hi all,

is there any where I can find pointers/program/script to do automated casava or FASTQ file generation ...upon completion of a run?

Meaning, if machine fishiness transferring file to a directory then automatically it start BCL to FASTQ conversion and if needed start alignment ?

Please let me know ..it would be a great help,

Thanks,
Saurin

simonandrews · 01-12-2012, 01:05 AM

If you want to start this automatically you'll have to have a small daemon running which can poll for new run folders appearing, and then wait until they're full to start the processing.

There was a previous thread which went through the various flag files which the Illumina software generates to tell you when the run is complete so you could pick out the ones which are appropriate for the platform(s) you run.

GenoMax · 01-12-2012, 04:27 AM

You would also need a way to generate the correct Samplesheet.csv file and make it available (for each flowcell(s)) so the right makefiles can be generated to start the processing.

sdj · 01-12-2012, 07:02 AM

thank you all..sure, I will look in to that

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01-11-2012, 12:52 PM	#1
sdj Junior Member Location: usa Join Date: Jul 2011 Posts: 3	automated pipeline casava or FASTQ script/program Hi all, is there any where I can find pointers/program/script to do automated casava or FASTQ file generation ...upon completion of a run? Meaning, if machine fishiness transferring file to a directory then automatically it start BCL to FASTQ conversion and if needed start alignment ? Please let me know ..it would be a great help, Thanks, Saurin

01-12-2012, 01:05 AM	#2
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	If you want to start this automatically you'll have to have a small daemon running which can poll for new run folders appearing, and then wait until they're full to start the processing. There was a previous thread which went through the various flag files which the Illumina software generates to tell you when the run is complete so you could pick out the ones which are appropriate for the platform(s) you run.

01-12-2012, 04:27 AM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	You would also need a way to generate the correct Samplesheet.csv file and make it available (for each flowcell(s)) so the right makefiles can be generated to start the processing.

01-12-2012, 07:02 AM	#4
sdj Junior Member Location: usa Join Date: Jul 2011 Posts: 3	thank you all..sure, I will look in to that