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  • .bcl to *qseq.txt conversion

    We are just starting to look at the informatics needs for supporting a HiSeq 2000. Does anyone have estimates for time and processing requirements to do the .bcl to *qseq.txt file format conversion?

    Thanks

  • #2
    Less than an hour per paired-100 flowcell on a reasonably fast cluster. We put each flowcell on a single node (8 cores) and it finishes in about 40 minutes.
    HudsonAlpha Institute for Biotechnology
    http://www.hudsonalpha.org/gsl

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    • #3
      Thanks

      Thanks for the time estimates. Do you also have any estimates as to how long it takes to demultiplex an 8 sample (or 12), per lane, run?

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      • #4
        Demultiplexing is pretty fast but depends on what barcoding method is being used.

        Whose barcodes are you using? If it is Illumina's indexing using the 3 reads, have you used them in the past? If not, now may not be the best time to start. I would wait a couple months and then re-evaluate barcode methods. If it is the adaptor-based barcodes, demultiplexing a 7bp barcode using typical Hamming error correction takes about 30 minutes for a 12-plex.
        HudsonAlpha Institute for Biotechnology
        http://www.hudsonalpha.org/gsl

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