Genomics Aotearoa's repositories
metagenomics_summer_school
Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in December
environmental_metagenomics
A quick workflow to get researchers started with the bioinformatic pipeline used in the Environmental Metagenomics program.
methods-and-musings
A (growing) collection of information contributed by Genomics Aotearoa members. Semi blog post style bites of content.
High-quality-genomes
This repository aims to hosting workflows/codes that have been developed for GA high-quality-genome projects.
long-read-assembly
Long-read assembly workshop
shell-for-bioinformatics
Intermediate-Advanced shell for Bioinformatics
Workshop-Bash_Scripting_And_HPC_Job_Scheduler
A workshop to get you started with automating your data analysis work in a High Performance Computing environment
data-management-resources
Repo supporting the manuscript 'Journeying towards best practice data management in biodiversity genomics'.
hts_workshop_mpi
Training materials for the 2023 HTS Plant Health and Environment Laboratory workshop
Nextflow_Workshop
A workshop to help you integrate Nextflow in your analysis workflows for reproducible and scalable pipelines.
Pangenome-Graphs-Workshop
This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.
AGM-workshop-2023
Reproducibility with Nextflow and nf-core, structured for the one-day AGM training day workshop
GenomicsAotearoa.github.io
Code and files for Genomics Aotearoa github.io website
IndigiDataAotearoa_IntroToR
Intro to R coding block for Indigidata Aotearoa
Introduction-to-Bash
Introduction to the Command Line for Genomics
Introduction-to-R
Introduction to R
intro-to-containers
Introduction to Software containerisation and some of the container platforms such as Apptainer , Docker
long-read-assembly-one-day
Long-read assembly workshop modified to run in a single day
long-read-microbial-isolate-genomics
Sequence processing workflow for samples obtained from microbial isolates sequenced using long-read technology.
nesi-jupyter
NeSI Mahuika cluster Jupyter login details
Nextflow-Developer-Workshop
Best practices for developing your pipelines with Nextflow and nf-core
Outlier_Analysis_Workshop
Outlier analysis workshop and research project developed under the AES ERC Networking Grant Scheme.
RNA-seq-workshop-on-demand
RNA-seq Data Analysis workshop, modified to run on the OnDemand training platform.