Sequencing Project Management Using the Staden Package

This course will introduce the Staden package of programs for sequence trace file interpretation. You will learn view or edit ABI trace files and understand how to assemble individual reads into a contiguous sequence.

Introduction - The Staden package of programs are used for the interpretation, screening and assembly of sequence trace files and the management of large-scale sequencing projects. The Staden package is available on the CBRG Unix server using your molbiol account.

The output from other makes of automatic sequencer can also be processed by these programs, as can data generated by manual sequencing methods. The programs are suitable for both large and small-scale sequencing projects. The package also contains novel methods for automatic detection of point mutations by the analysis of ABI trace data.

Participants on the course will be guided through practical exercises during which they will process a substantial set of sequence data obtained from an ABI automatic sequencing machine. You are also encouraged to bring along any sequencing data that you may have - there is usually time to discuss problems arising from particular data sets as well as going through the standard exercises.

Date - This one day course will be held on Friday, 12th January, 2007 and will start at 9:30

Location - This course will be held in the Medical Sciences Teaching Centre on South Parks Road (behind the Sir William Dunn School of Pathology - see map).

Although this software is still very much in use by a variety of research groups, the MRC removed funding for this project in April 2003 and there is no direct support from a development group. However, the software has made open source and work is coordinated by one of the original package authors.

Links:

• Staden package home page