Alfx and Phred

Phillip San Miguel pmiguel at bilbo.bio.purdue.edu
Mon Sep 28 16:00:39 EST 1998


Does anyone know if Phred will read Alfx (.alx or .alf) files?  I
mainly ask because some documentation I found (see below) at the URL

http://bozeman.mbt.washington.edu/phrap.docs/phred.html

seems to suggest that Phred will read Alf format files.  Specifically:

"Phred can read trace data from SCF files, ABI model 373 and 377 DNA
sequencer chromat files, and ALF DNA sequencer data files,
automatically detecting the file format."
  Any information would be appreciated.
Phillip San Miguel



*|***************************************************************************|*

*|
|*
*|   Program:
phred                                                          |*
*|   Version:
0.960108                                                       |*
*|
|*
*|   Copyright (c)  1992-1996 by Phil Green and Brent
Ewing.                 |*
*|   All rights
reserved.                                                    |*
*|
|*
*|   Redistribution of source code or executables, or use for any
purpose    |*
*|   other than calling DNA bases in an academic laboratory as part
of       |*
*|   strictly academic grant-funded or university-funded research
requires   |*
*|   explicit written permission
from                                        |*
*|
|*
*|   Phil
Green                                                              |*
*|   Department of Molecular
Biotechnology                                   |*
*|   University of
Washington                                                |*
*|   Box
357730                                                              |*

*|   Seattle, WA
98195-7730                                                 |*
*|
|*
*|
phg at u.washington.edu
|*
*|
|*
*|   Portions of the code or ideas are due to Dave Ficenec,
LaDeana          |*
*|   Hillier, Mike Wendl, and Tim Gleeson.  These are
indicated              |*
*|   specifically in the relevant source
files.                              |*
*|
|*
*|***************************************************************************|*



PHRED Documentation
-------------------

1. Introduction.

   Phred reads DNA sequencer trace data, calls bases, assigns quality
   values to the bases, and writes the base calls and quality values
to
   output files.  Additionally, it can display the traces and base
calls
   on displays equipped with X11 servers.  Phred can read trace data
from
   SCF files, ABI model 373 and 377 DNA sequencer chromat files, and
   ALF DNA sequencer data files, automatically detecting the file
format.
   After calling bases, phred writes the sequences to files in either
   FASTA format or the format suitable for XBAP.  Quality values for
the
   bases are written to FASTA format files, which are used by the
sequence
   assembly program phrap to increase the accuracy of the assembled
   sequence.  The sequence and quality values can be written to PHD
files
   as well.






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