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 |
