Annotation Unix Worksheet
Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.
Chris Shaffer
Introduction to UNIX Exercise
A simple exercise on using simple Unix commands to navigate to different directories and manipulate files.
Unix Commands: Quick Reference Sheet
A Unix reference sheet for commonly used Unix commands.
Command Line Unix: BLAST, RepeatMasker, Herne
PowerPoint presentation with instructions for running BLAST, RepeatMasker, and the BLAST output viewer Herne on the command-line.
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.