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.
Home » Drosophila »
Drosophila
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.
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.
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.
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.
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.
Overview of the Drosophila modENCODE Hybrid Assemblies
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.