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Chris Shaffer

Finishing Lab Practice Using a Mouse Contig

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.

The D. grimshawi dot chromosome

This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.

GEP Misassembly Tools User Guide

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.

Finishing Checklist

Students should complete all items on this checklist before submitting the project back to the GEP.

Strategies for Finishing Hybrid Assemblies

This document contains advice on the strategies students can use to resolve common problems they may encounter during sequence improvement.

Calling Additional Reads

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.

PCR Primer Selection Guide

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.

Sequence Improvement Protocol for GEP Hybrid Assembly Projects

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.

Drosophila Finishing Problem Set

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.