Version: 8
File Name: README.SQPR.v8
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SQPR: Sequence Quality Plate Reader

SOFTWARE SCRIPTS FOR QUALITY CHECKING OF HIGH-THROUGHPUT NUCLEIC 
ACID SEQUENCERS. 2001. BioTechniques. Vol 30, No. 6.

GR Lazo, J Tong, R Miller, C Hsia, C Rausch, Y Kang, and OD Anderson.
USDA ARS Western Regional Research Center, 800 Buchanan Street, 
Albany, CA 94710-1105.

Address correspondence to: Gerard R. Lazo (lazo@pw.usda.gov).
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Files Contained within directory: 

	- dirdisplay.cgi
	- runphred.cgi
	- fastadisplay.cgi
	- phddisplay.cgi
	- redo.cgi
	- trace.cgi
	- trace1.cgi
	- trace2.cgi

	- GolbalVariables.lib
        - subparseform.lib

	- README.SQPR.v8
	- README.SQPR_name_syntax

Description of the Programs:

This set of programs work under a cgi-bin directory of a web server
and utilizes the phred program to read sequencing trace file data 
from high-throughput automated sequencers and archives the data for 
assessing the quality of sequencing runs.

dirdisplay.cgi   : Displays a list of unprocessed datafolders.
runphred.cgi     : Initiates phred analysis on the selected datafolder 
                   displayed by dirdisplay.cgi.
fastadisplay.cgi : Displays a list of all the phred-analyzed datafolders.
phddisplay.cgi   : Displays a graphical representation of the analyzed 
                   datafolder shown by fastadisplay.cgi. Displays are 
                   of 96-samples at a time in standard 96-well format, 
                   or 96 samples from a 384-well formatted plate which 
                   is automatically detected.
redo.cgi         : If empty cells appears, an option is presented to 
                   erase data results so that they may be re-analyzed by 
                   the runphred.cgi script.
trace*.cgi       : These files are activated from the phddisplay.cgi 
                   display to initiate a java applet to display 
                   individual sequence traces.
GolbalVariables.lib : File for configuring the program scripts to 
                   read and write in data directories, and for locating 
                   executable and configuration files.
subparseform.lib : Used to create HTML pages
README.SQPR.v8   : This file.
README.SQPR_name_syntax : This file explains the default syntax for 
                   for naming sequence files and directories.

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 This software is a "United States Government Work" under the terms 
 of the United States Copyright Act. It was written as part of official 
 duties performed by a United States Government employee(s) and thus 
 cannot be copyrighted. This software is freely available to the public 
 for use. The United States Department of Agriculture and the U.S. 
 Government have not placed any restriction on its use or reproduction. 
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