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https://github.com/NorwegianVeterinaryInstitute/BioinfTraining

Repository for bioinformatics training at the Norwegian Veterinary Institute
https://github.com/NorwegianVeterinaryInstitute/BioinfTraining

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Repository for bioinformatics training at the Norwegian Veterinary Institute

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README 

        
# Bioinformatics training at the Norwegian Veterinary Institute



## Purpose

At the Norwegian Veterinary Institute, we are now starting an internal course in bioinformatics. This

repo will contain information, documentation, tutorials etc for this course.



## Instructors



The instructors are:



  * Karin Lagesen - comparative genomics and main organizer

  * Arvind Sundaram - transcriptomics

  * Thomas Haverkamp - metagenomics



## Practical information



# Variant calling and phylogeny

  * [Use of SNIPPY](variant_calling_snippy.md)



# Small how-tos for various processes



  * [Use of mash](mash.md)

  * [Use of conda](conda.md)

  * [Mapping and visualization](assembly_visualization.md)

  * [Tree generation and visualization in R](R_trees.md)



## Course pages



We have created specific pages for each part of the course.



  * [Common introduction](introduction.md)

  * [Technical tricks and hits](techstuff.md)

  * [Comparative genomics](compgenomics.md)

  * [Metagenomics](metagenomics.md)

  * [Transcriptomics](transcriptomics.md)



### Messages



We will keep an archive of outgoing practical messages, like homework etc,

[on this webpage](messages.md). Note, some information might be redacted for

information security reasons.



### Etherpad



An Etherpad is a collaborative document where all can write down notes,

tips, hints, links etc. Please note, this document is public, and hence,

you should not write anything there that you wouldn't talk about on

the bus on your way to work!



[You can find the etherpad for this course here](https://etherpad.wikimedia.org/p/nvi-bioinf)



## Tentative schedule



| Date| Subject| Taught by|

|------|-------|----------|

|2017-11-30 (full day)| Virtualbox, File system, UNIX part I |Thomas/Karin|

|2017-12-07 (full day) | UNIX part II, Abel, SLURM, ssh, File transfer (scp, rsync), editor (nano)| Arvind/Karin|

|2017-12-14 (full day)|QC - FastQC, Trimmomatic and cutadapt, duplicates (samtools)|Arvind|

|2018-01-11 |Intro to R|Thomas|

|2018-01-18| Jupyter as interface, Intro to Python|Karin|

|2018-01-25|File formats|Arvind|

|2018-02-01 to 2018-03-29|Case study (8 Weeks) | All|

|2018-03-29 and onwards |Working with own data | All|



### Computers



All participants will be handed a laptop with Virtualbox installed. All

participants are expected to handle this laptop with care, and to ensure that

nobody gets access to it. This laptop is yours for the duration. You have admin

on this computer, but don't take this to mean that you can install whatever you

want. Last but not least, this computer should only be used on the wireless

network at the Institute, and should not be plugged in the wall.



Please note: do not keep data on this laptop that you cannot afford to lose.

This laptop is not a storage device - this is a tool used for processing data,

not for storing it.



### Virtualbox

The main reason you are given a separate computer to work on is because we

will be using the software called Virtualbox. This is software that we are not

allowed to use on computers connected to the network at the Institute.



Virtualbox is a program that enables you to have a computer running virtually

inside your computer. You will "install" a specific version of linux inside

virtualbox. This is what we will use to interface with the cluster that we will

use for processing the data.



### Abel

We will use the University of Oslo's High Performance Computing cluster for

most of our work. For more about how Abel works. see here.



Please note: transfer and storage of data on abel is only allowed with prior

approval by Karin.



You can find out more about [how to use abel here.](https://github.com/NorwegianVeterinaryInstitute/Info/wiki)



## Contact



To contact the instructors, please leave an issue in the github repo. Karin is

also available on twitter, as @karinlag .



Veterinary Institute people should contact the instructors on the instructors

email list, or contact Karin via her vetinst email.



## Course Navigation: