SGBC Bioinformatics Course

This website is a collection of lectures and tutorials given during the annual Bioinformatics course given at SLU by the SGBC.

Course information

• What: Bioinformatics, 15 ECTS
• Where: SLU, Campus Ultuna, Uppsala, Sweden
• When: 21 Jan - 25 March 2019
• Course page: link
• Course schedule: link (Google docs)

Welcome to the course!

Table of Content

First Week

• Biological Databases
• Online Blast
• Introduction to the command-line
• Cloud Computing
• Installing Software
• Command-line Blast

Second week

• Sequencing Technologies
• Quality Control
• De-novo Genome Assembly
• Assembly Challenge
• Genome Annotation
• Pan-genome Analysis
• Nanopore Sequencing

Third week

• Genome Browsers
• R

Fourth week

• RNA Sequencing
• Genome Annotation (NBIS)

Fifth week

• Phylogeny
• EMBOSS
• UGENE

Sixth week

• Introduction to proteins analysis
• Metabarcoding
• Metagenome assembly
• Comparative metagenomics

License

Unless stated otherwise, all the lessons are licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

Contributors

The following people have contributed to these course material, in no particular order:

• Hadrien Gourlé
• Juliette Hayer
• Oskar Karlsson
• Jacques Dainat