SQPR: Sequence Quality Plate Reader

Please see:

Lazo, G.R., Tong, J., Miller, R., Hsia, C., Rausch, C., Kang, Y., and Anderson, O.D. 2001.
Software scripts for quality checking of high-throughput nucleic acid sequencers.
BioTechniques 30(6):1300-1305.

ABSTRACT:

We have developed a graphical interface to allow the researcher to view and assess
the quality of sequencing results using a series of program scripts developed to
process data generated by automated sequencers. The scripts are written in Perl
programming language and are executable under the cgi-bin directory of a world-wide-web
(WWW) server environment. The scripts direct nucleic acid sequencing trace file data
output from automated sequencers to be analyzed by the phred molecular biology program
and are displayed as graphical hypertext mark-up language (HTML) pages. The scripts are
mainly designed to handle 96-well formatted microtiter dish samples, but the scripts are
also able to read data from 384-well formatted microtiter dishes 96 samples at a time.
The scripts may be customized for different laboratory environments and computer
configurations. WWW links to the sources and discussion page are provided.

Program Sources

Feedback Bulletin Board for Comments and Questions

The Bulletin Board is located here

Sample Demonstration of the Software

A sample of the processing (this is just a mock run in this example)
dirdisplay.cgi: To start, you would first select the script to display the trace file data directories (TFDD) which contain *.ABI or *.SCF trace files available for phred processing.
Select dirdisplay.cgi (listed is sample data).
Runs 608, 680, 681, and 682 are part of a 384-well plate run.
Runs 663 and 675 are each 96-well formatted plates.
runphred.cgi
fastadisplay.cgi: This will list the trace file data directories (TFDD) which have already been processed by phred and have results present in the Phred-analyzed Output Data Directory (PODD). Selecting a listed directory will initiate the phddisplay.cgi script.
Select fastadisplay.cgi to display processed TFDDs.
phddisplay.cgi