Consed

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.

Finishing Lab Practice Using a Mouse Contig

Students can practice using Consed by working on a mouse contig. This exercise poses various challenges that students may encounter when working on their own projects.

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.

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.

Drosophila Finishing Problem Set

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.