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Reconcile Sequence Improvement Projects

All GEP projects are completed at least twice independently by GEP students. This document describes how to check two or more submissions of a finishing project for congruence. Ordinarily this is done centrally at Washington University, but in some cases may be of interest at a given school.

A Complex Drosophila Fosmid

This fosmid from Drosophila virilis assembles into three contigs (a yellow clone). In this exercise, students must generate a final assembly by closing a gap, dealing with a mis-assembly, and improving low quality regions. Snapshots of the different stages of the assembly are stored as separate ace files.

A Simple Drosophila Fosmid

This fosmid from Drosophila virilis assembles into a single contig (a green clone). In this exercise, students will need to identify regions in the assembly where additional data is needed and design additional sequencing reactions to bring the contig up to quality standards.

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.

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.

Finishing Checklist

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

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.