Hi all, in order to produce some QC report we currently use the ShortRead qa pipeline, like this:

qual<-qa(PATH_TO_GERALD_DIRECTORY, pattern=".*export.txt",type=c("SolexaExport"))

We produce eland alignments only for this purpose and it takes so much time. Also, the QA process is taking more and more time as the throughput of Illumina machine increases... We've been trying to run with BAM files (which is the default for us, as we use bwa only), but we can't get the same report with same sections... Which is the fastest way to have decent QC without the Illumina pipeline?

THanks


d
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Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
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tel.: +39(02)574303007
e-mail: davide.cittaro@ifom-ieo-campus.it
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