BINF 6215

BINF 6215

This is the game plan for BINF 6215 — Bioinformatics Pipeline Programming. Links to these posts will also be provided in Moodle, but this post will serve as a directory for the course. Links will go live as the tutorials are ready.

The recommended textbook is Practical Computing for Biologists by Haddock and Dunn. We are not going to work through the entire book, but there are some chapters in there that will be a useful reference for you in your future work, so you should definitely get it.

Some suggested NGS datasets
General tips on taming Illumina datasets for assembly applications

Class Date Morning Afternoon
Monday July 21 Build your first workflow Things you can do on your Mac — UNIX style
Format conversion at the command line
Tuesday July 22 Basics of CLC Workflows — with Naomi Thomson, CLC Genomics Variant detection workflow in CLC
Wednesday July 23 CLC ChIP-Seq analysis workflow Workflows with the transcriptomics tools in CLC
Thursday July 24 Bioextract — with Dr. Carol Lushbough, USD Bioextract — with Dr. Carol Lushbough, USD
Friday July 25 Bioextract — with Dr. Carol Lushbough, USD Bioextract — with Dr. Carol Lushbough, USD
Monday July 28 Data deposition day [1][2][3]
Automating a repetitive task
Unix command line basics
Tuesday July 29 Command line pipes and shell scripting basics Figuring out bioinformatics command line software
Wednesday July 30 Driving software with shell scripts
Command line variant calling
Trinity and Corset at the command line
begin command line challenge project
Thursday July 31 bpipe for script management More workflow implementation in bpipe
continue command line challenge project
Friday Aug. 1 Working on Galaxy Main: Galaxy 101 Working on Galaxy Main: Galaxy NGS 101 (Synechocystis version)
Monday Aug. 4 Get your own Galaxy
Galaxy Variant Detection Tutorial
Galaxy Assembly Tutorial
Tuesday Aug. 5 You solve it/maker day Follow up on data deposition
Comments are closed.