SCF/ABI support for Delphi comunity

2005-09-02
2013-04-18
  • Nobody/Anonymous

    Hi. I want to make a library for my self and for Delphi comunity.
    I allready have support for SCF, SEQ and ABI files (read/write) and conversion between ABI <-> SCF.

    The problem is, I can't find support for QV (quality values).
    How are this stored (especially) in ABI files?

    Can somebody provide some (good) documentation about ABI file format ?

    Thanks.

     
    • Nobody/Anonymous

      I forget to write my email:

      newfedra@yahoo.com

       
    • James Bonfield

      James Bonfield - 2005-09-05

      Clark Tibbets (or TIbbetts?) did lots of work on the ABI format and also published it. I've also got a variety of simple command line tools to investigate the ABI contents. It's useful background reading, but so much has been added since then (including confidence values).

      The getABIfield program (I'm not sure which version of the code I added this, but it'll certainly be in the windows latest beta release) dumps out the "directory" contained within the ABI file. It then allows extraction of any individual object within it.

      The confidence values in ABI are stored as PCON. There's PCON 1 and PCON 2 to mirror PBAS 1 and PBAS 2. I assume this stands for Phred CONfidence as they use the same scale. I believe these were added at the time ABI made BioLIMS so that people could convert Phred basecalled data back to ABI before importing.

      I'm trying to recall if KB outputs the same channels too. I know Trev handles it so I'm fairly confident it's the same PCON channels.

      James

       

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