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index.Rmd
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---
title: "OUCRU-MORU bioinformatics workshop"
date: '`r format(Sys.time(), "%d %B, %Y")`'
---
# Introduction {-}
This is the website for the OUCRU-MORU bioinformatics workshop.
This course is intended to take total beginners in bioinformatics and give them a grounding in the fundamentals.
By the end of the 5 day course, participants should be able to work on the command line and run and interpret some fundamental bioinformatics software.
If you have any questions about this material, please contact pashton at oucru dot org or liz at tropmedres dot ac, or tweet us @flashton2003 & @embatty.
The data for the course is available [here](https://www.dropbox.com/sh/qd13lyrz21wwine/AADyOzVmRUAtQrhS5-AJjepqa?dl=0) (around 5GB).
# Course content {-}
**Day 1**
AM - Intro to genome sequencing, file formats and CLIMB, draw your career path
PM - Command line practical
**Day 2**
AM - Sequence quality control, speciation
11.30am - Break for OUCRU academic meeting
PM - Genome assembly
**Day 3**
AM - BLAST
11.30am - Break for OUCRU academic meeting - Prof Seemann
Post-lunch seminar - Trung Nguyen Vinh
PM - Annotation, visualisation, core/pan genome analysis
**Day 4**
AM - Alignment and variant calling
Post-lunch seminar - Hao Chung The
PM - Phylogenetics and outbreak investigation, viruses
**Day 5**
AM - Group presentations; you will be divided into teams and have to design a bioinformatics strategy to solve a specific microbiological question, and then present back to the whole group
12.30pm - OUCRU Academic meeting
PM - free time to talk to instructors about bioinformatics approaches to take with your own datasets or biological questions
# License {-}
This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/).