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.
This document illustrates how students can apply the sequence improvement protocol described in the “Sequence Improvement Protocol for GEP Hybrid Assembly Projects” document to specific problems in a D. biarmipes sequence improvement project. Specifically, the walkthrough describes techniques for correcting consensus errors and for closing gaps.
A training document similar to “An Introduction to Consed,” this document contains a more detailed walkthrough that explores additional functions available in Consed.
A walkthrough that illustrates how students can use Consed to identify problematic regions in a genome assembly and strategies students can use to address these problems.
This document is a basic introduction to Consed, a program that allows users to visualize and manipulate a genome assembly. It provides screenshots of the various windows and points out the various functions available.
Dr. Justin R. DiAngelo (Penn State Berks) has developed an exercise for the Sanger Sequencing and Next Generation Sequencing video tours.
This PowerPoint presentation discusses the basic directory structure required by Consed and the UNIX commands used to launch Consed.
