This document is a basic introduction to Consed, a program that allows users to visualize and manipulate a genome assembly. It provides screenshots of the various windows and points out the various functions available.
The lecture notes from a presentation by Bob Fulton that point out some of the more advance 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 work on their fosmids.
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 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 (walk-throughs) of challenging fosmid assemblies.
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.