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Chris Shaffer

Annotation Unix Worksheet

Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.

Introduction to UNIX Exercise

A simple exercise on using simple Unix commands to navigate to different directories and manipulate files.

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.

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.

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.

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.

Calling Additional Reads

Students will typically need to request additional sequencing reactions in order to improve the quality of an assembly. This document describes some of the key considerations that students should keep in mind when they design oligonucleotide primers.