Finishing Strategy

Common Finishing Errors

This PowerPoint presentation describes the common errors observed in student finishing projects.

Fulton Lecture Notes

The lecture notes from a presentation by Bob Fulton point out some of the more advanced features of Consed, the base caller phred, and the assembler phrap. This document should be read after students have some experience using Consed but before they begin working on their fosmids.

Restriction Digests: A Tool to Check Your Findings

One of the main tools used to verify the correctness of a genome assembly is comparison of an in-silico restriction digest to the real restriction digest data generated by the WU Genome Center. This document also covers how students can use the restriction digest data early in the assembly process to determine the number of copies of repeats in a given cluster or to estimate gap sizes.

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.

Workflow to Resolve Misassembly

A flowchart that illustrates the key decisions and strategies when dealing with misassemblies that are caused by collapsed repeats.

Common Misassembly Protocols

This document describes a list of protocols that are frequently used to resolve misassembly.

Identifying and Sorting Tandem Duplications and an Inverted Repeat

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.

The Finishing Report

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.

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.

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.