Human Genome Sequencing Automation - Automation Software Packages

The UTSW GESTEC has produced several packages of software that may have some universal utility. These software modules complement some of the other generally available software (phrap, segmap, gram, staden) that are used in mapping and sequencing projects. Following are descriptions of some of the software, what they do, and what is requires to run them. These programs can be obtained by contacting the webmaster.

MatrixMechanic

This program was written to improve data quality from samples run on ABI 377 sequencers with the XL upgrade by recalulating the matrix of the gel file based on 5 points specified by the user. See the "readme" file for more information.

Development environment: Metrowerks Codewarrior

UnShift

This program was written to save gel files created by ABI 377 sequencers with the XL upgrade (i.e. using ABI collection software version 2.0) that have had sections shifted horizontally. For more information open the "readme" file included with the archive.

Development environment: Metrowerks Codewarrior

GelWeld

This program was written to save data collected by ABI 377 sequencers with the XL upgrade (i.e. using ABI collection software version 2.0) that has been "split up" into two or more ABI gel files. This can be caused by power blinks, disk fragmentation, and many other problems.

Development environment: Metrowerks Codewarrior

Gel Rescuer

This program saves ABI gel files whose resource forks have been damaged, but whose data forks are still intact.

Development environment: Metrowerks Codewarrior

Quicksheet

This 4th Dimension program automates the production of ABI Sequencer Sample Sheets. The user interface is used to quickly set the ABI machine, the plate to be sequenced, and other parameters. It then generates the sample sheet files that can be moved to the appropriate instrument.

Development environment: 4th Dimension

Distributor

This script is used to separate many sets of run files generated from ABI 377 tracking and extracting analysis. Trace files are prepared to be sent over the network to an assembly workstation, other files are archived temporarily to give an automated backup system time to record them, and other files are trashed. Some error checking is done.

Development environment: AppleScript