ABI 3700 and Phred/Phrap

Phillip San Miguel pmiguel at purdue.edu
Sat Jun 12 14:28:54 EST 1999

>  Stephen R. Lasky wrote :
>  We've been running phredPhrap on the 3700 files and gotten pretty good
>  results (when I called Q>20 values of about 400 by eye, phred called 406
>  and 422 (for eg)).  Lee Rowen has talked to Brent Ewing about retraining
>  phred on 3700 chromats.  It turns out that Genoscope has sequenced and
>  submitted (and is therefore presumably high quality sequence) a bac on
>  chromosome 14 that overlaps one of our bacs by a significant amount, so
>  we are going to run 10-12 plates of sequence on the 3700 and use the
>  Genoscope sequence as a known and give Brent the dataset.
> [...]

    So that would be using LiCor sequence as a known against which 3700 sequence can be scored?  I
can almost see the LiCor advertisment now...
    Is there any reason ABI doesn't provide software that will generate quality scores for each
base that can be used by Phrap?

Phillip San Miguel
Purdue Genomics Center

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