norwegianveterinaryinstitute Goto Github PK

Name: Norwegian Veterinary Institute

Type: Organization

The Norwegian Veterinary Institute

The Norwegian Veterinary Institute is a biomedical research institute, and the national leading centre of expertise in biosecurity in fish and land animals. The aim of the Institute is to become Norway’s centre of preparedness for One Health.

This github site is where the Institute keeps code and other resources. We welcome comments and feedback on our work. The best way to do that is to submit an issue in the relevant repo.

Major groups

We have several subgroups that use the NVI github repo.

The Bioinformatics group

Bioinformatics is a growing field at the Institute. We currently have three dedicated people working on bioinformatics, and quite a few projects in that area.

Salmon lice group

We are also quite active in the salmon louse area, and work on that can also be found in the NVI repos.

Support or Contact

For more general questions about NVI on github, contact karin dot lagesen at vetinst dot no.

Norwegian Veterinary Institute's Projects

2021-teaching

Repository for teaching git

alppaca

A tooL for Prokaryotic Phylogeny And Clustering Analysis

assemblage

bifrost

bioinftraining

Repository for bioinformatics training at the Norwegian Veterinary Institute

cgmlst_tree

Nextflow and R - rewritting of script to create hierarchical clustering - NJ or UPGMA trees from chewBBACA cgMLST clustering

count-org-loc

Count total lines of code across a GitHub organization

cwdsurveillanceusinghunters

delicious

Share your recipes - version control your recipes. I suspect most of the practical version control will be focused on cakes. But other recipes are welcome, particularly if they are excellent and take almost no time to prepare. Share your tips and tricks! We like efficiency. You can also add conversion, cooking time estimators scripts if you want … You are also most welcome to use this repository as a training tool to learn git.

demultiplexrawsequencedata

A workflow automation script: demultiplex the library sequence, run quality checks, deliver to archiving and processing afterwards

digivet_d2.3_amu

DigiVet deliverable 2.3 for AMU. An example of how to transform AMU raw data into standardised data using Norwegian data.

dpi

Differences between Pairs of Isolates

ellipsis

Plasmid assembly, gene identification and annotation pipeline

ffpa_nextflow

This repository contains the nextflow implementation of the Full Force Plasmid Assembler Pipeline

fish_mortality_api

fullforceplasmidassembler

Full Force Plasmid Assembler Tool

ggtrevextra

Package preparation: for analysis visualization of phylogenetic trees, distances, phylogeography ...

hafnia_reports_2024

hkaspersen_thesis

Repository for PhD Thesis of Håkon Kaspersen

hunting_wildlife_for_disease_detection

R-scripts and data files to reproduce analysis from the paper Hunting wildlife for disease detection.

irida-nvi-serotypefinder

irida-plugin-fastq-fasta

Test plugin to make our hands dirty in learning how to develop irida-plugin

irida-plugin-kleborate

irida-plugin-listeria-typing

IRIDA plugin for Listeria monocytogenes typing

irida-plugin-nvi-mlst

irida-plugin-readsqc

irida-plugin-respointfinder3

EFSA 2023: Takes Fastq pairedend reads as input and compares against ResFinder and PointFinder database. LineList header prefix is "RPF2403". ResPointFinder tool version: 4.4.2, ResFinder DB version: 2.2.1, PointFinder DB version: 4.0.1 DisinFinder DB version 2.0.1