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ABI QC

About this program

This program was requested by the Yorkshire Regional Genetics Service (YRGS) for their quality control procedure. When the ABI software base calls a trace file it calculates a signal to noise ratio for each channel (A, C, G and T), which is then stored in the AB1 file. If this value falls below 100 for any of the channels in a file, the YRGS suggest that, that sequence has failed QC. The program reads all the AB1 files in a folder and then places the results in a tab-delimited text file called results.xls. This file is then saved to the same folder as the AB1 files.

It must be noted that this is just one step in their QC procedure and that traces which past this test may still have no useable sequence data. This program is currently been used by other Genetic Services around the UK. Some of these centres use a different cut off. To stop the cut off value been incorrectly set by a user it is not adjustable by the end user. If you require a different value email me and I'll change the value.

This program is only suitable for people that do a lot of sequence analysis and require an initial screening procedure for their QC system.

insilicase icon This program comes in two versions; version 1 requires .Net version 1.1 which should be standard on all XP computers. The other version requires .Net version 2.0 which may not be on all XP computers, but will be on Vista and Windows 7 computers. If you use an older version of windows you may need to install the .Net frame work (see troubleshooting). Other than different .Net requirements there is no difference between the two versions.

Download ABI_QC_vers_1.1.zip

Download ABI_QC_vers_2.0.zip

Instructions

To check ABI peak heights against a ‘blank’ file press ‘Blank’ and select the blank file. This will then be compared to all the other AB1 files in the same folder as this file. Otherwise, to check the peak heights press ‘No Blank’ and select the folder containing the files. The results will be written to a tab delimited text file called 'results.xls' in same folder. This file will open in Excel as a spreadsheet. The programme also calculates the ratio of faintest trace / brightest trace (%).



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