Staden's package & ALF

James Bonfield jkb at mrc-lmb.cam.ac.uk
Thu Jun 18 03:15:47 EST 1998

In article <199806171522.MAA15815 at mutum.dcc.unicamp.br> setubal at dcc.unicamp.br (Joao Carlos Setubal) writes:
>I need to know how the Staden package handles chromatogram curves from
>ALF (Pharmacia) sequencing machines. Specifically, can it somehow
>assign quality values to the bases as Phil Green's phred program does?

The Staden Package includes no base calling functionality, and has no
(reliable) assignation of quality values. However it can (as have
previous releases) read ALF files.

Phil Green's phred program can read SCF files. I think that Pharmacia
can now write SCF files. The Staden Package also includes a program to
convert ALF files to SCF files. However I would not expect phred to
work particularly reliably on a converted ALF file as it has been
tuned to work on the processed output of ABI files (and ABI files
converted to SCF). I doubt that Pharmacia use identical processing to
ABI. It's probably worth giving it a try though.

Note that the Staden Package does not require the use of quality
values, but their presence would help to obtain a better quality
consensus sequence.

We know of work in progress in rewriting the ALF base caller. The new
software will assign quality values, although I do not know how
compatible they are to those assigned by phred.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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