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.
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.
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.
This PowerPoint presentation provides a general overview of the hybrid assemblies produced by the Baylor College of Medicine Human Genome Sequencing Center as part of the Drosophila modENCODE project. This presentation provides a brief introduction to the source of the raw sequence data and the protocol used by BCM-HGSC to construct the draft D. biarmipes genome assemblies.
Students can practice using Consed by working on two Drosophila projects. This exercise poses various challenges that students may encounter when working on their own projects.
