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Old 01-11-2012, 12:52 PM   #1
Junior Member
Location: usa

Join Date: Jul 2011
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Smile 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 would be a great help,

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Old 01-12-2012, 01:05 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

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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.
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Old 01-12-2012, 04:27 AM   #3
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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.
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Old 01-12-2012, 07:02 AM   #4
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thank you all..sure, I will look in to that
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automated, casava, fastq, illumina

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