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.
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.
Students will typically need to request additional sequencing reactions in order to improve the quality of an assembly. This document describes some of the key considerations that students should keep in mind when they design oligonucleotide primers.
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.
This document contains advice on the factors that students should consider when designing PCR primers to resolve gaps and low quality regions. The document also includes the specific search parameters students should use to minimize the chance of off-target priming when designing PCR primers.
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.
This document describes the GEP protocol for improving the hybrid assemblies produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). This document is designed to work in concert with the GEP Hybrid Assembly Walkthrough that illustrates how students can apply this protocol to specific issues that they might encounter during the sequence improvement process.