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This section contains curriculum materials on sequence improvement of genome assemblies produced by Sanger sequencing.
Sequence Improvement of Sanger Assemblies
The D. grimshawi dot chromosome
Last update: 01/14/2009
This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.
D. mojavensis: Issues of Polymorphisms
Last update: 08/20/2009
This presentation discusses the potential sequence improvement issues caused by single nucleotide and insert polymorphisms in the D. mojavensis and D. grimshawi projects.
A Simple Drosophila Fosmid
Last update: 07/29/2012
This fosmid from Drosophila virilis assembles into a single contig (a green clone). The student will need to identify regions in the assembly where additional data is needed and design additional sequencing reactions to bring the contig up to quality standards.
A Complex Drosophila Fosmid
Last update: 07/29/2013
This fosmid from Drosophila virilis assembles into three contigs (a yellow clone). Students must generate a final assembly by closing a gap, dealing with a mis-assembly, and improving low quality regions. Snapshots of the different stages of the assembly are stored as separate ace files.
Finishing Lab Practice Using a Mouse Contig
Last update: 01/06/2007
Students can practice using Consed by working on a mouse contig. This exercise poses various challenges that students may encounter when working on their own projects.
Restriction Digests: A Tool to Check Your Findings
Last update: 01/27/2005
One of the main tools used to verify the correctness of a genome assembly is comparison of an in-silico restriction digest to the real restriction digest data generated by the WU Genome Center. This document also covers how students can used the restriction digest data early in the assembly process to determine the number of copies of repeats in a given cluster or to estimate gap sizes.
Fulton Lecture Notes
Last update: 01/30/2006
The lecture notes from a presentation by Bob Fulton that point out some of the more advance features of Consed, the base caller phred, and the assembler phrap. This document should be read after students have some experience using Consed but before they begin work on their fosmids.
Dye Chemistry Characteristics
Last update: 06/13/2008
This document illustrates some of the advantages and potential problems with the BigDye and dGTP chemistries.
Reconcile Sequence Improvement Projects
Last update: 02/19/2013
All GEP projects are completed at least twice independently by GEP students. This document describes how to check two or more submissions of a finishing project for congruence. Ordinarily this is done centrally at Washington University, but in some cases may be of interest at a given school.
Common Finishing Errors
Last update: 08/20/2009
This presentation describes the common errors observed in student finishing.