This fosmid from Drosophila virilis assembles into a single contig (a green clone). In this exercise, students 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.
This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.
A flowchart that illustrates the key decisions and strategies when dealing with misassemblies that are caused by collapsed repeats.
This document describes a list of protocols that are frequently used to resolve misassembly.
This document describes the list of tools developed by the GEP to facilitate incorporation of additional reads from the NCBI Trace Archive into a sequence improvement project. This document shows how to install the tools, and illustrates their use in two case studies (walkthroughs) of challenging fosmid assemblies.
Developed by the professional finishers at the WU Genome Institute (Holly Kotkiewicz and Jennifer Hodges), this walkthrough illustrates how you can use high quality discrepancies, Miniassembly, and cross_match to resolve a major misassembly in a D. ananassae project.
This document describes the final student written and oral reports required as part of the Bio 4342 course as taught at WU. In these reports, students describe their work on their fosmid, the challenges they encounter, and the solutions they developed to resolve these challenges.
Students should complete all items on this checklist before submitting the project back to the GEP.
This document contains advice on the strategies students can use to resolve common problems they may encounter during sequence improvement.
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.
