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.
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.