Repositories list

• Intermediate-R-Two-Day-Workshop

  Public
  Intermediate R structured to run over two half-days (9am - 1pm)

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

• Intermediate-R

  Public
  workshop-material

  HTML

  •

  GNU General Public License v3.0

  •3•2•0•0•Updated Feb 24, 2025Feb 24, 2025

• High-quality-genomes

  Public
  This repository aims to hosting workflows/codes that have been developed for GA high-quality-genome projects.

  high-quality-genomes

  HTML

  •10•6•0•0•Updated Feb 17, 2025Feb 17, 2025

• environmental_metagenomics

  Public
  A quick workflow to get researchers started with the bioinformatic pipeline used in the Environmental Metagenomics program.

  environmental-metagenomics

  HTML

  •6•10•0•0•Updated Feb 17, 2025Feb 17, 2025

• Introduction-to-R

  Public
  Introduction to R

  workshop-material

  Creative Commons Zero v1.0 Universal

  •2•2•0•0•Updated Oct 21, 2024Oct 21, 2024

• metagenomics_summer_school

  Public
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber

  workshopworkshop-materialenvironmental-metagenomics

  HTML

  •

  GNU General Public License v3.0

  •30•55•3•0•Updated Sep 5, 2024Sep 5, 2024

• IndigiDataAotearoa-IntroToShell

  Public
  workshop-material

  CSS

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated Aug 26, 2024Aug 26, 2024

• Workshop-Bash_Scripting_And_HPC_Job_Scheduler

  Public
  A workshop to get you started with automating your data analysis work in a High Performance Computing environment

  workshop-material

  HTML

  •

  MIT License

  •5•4•0•0•Updated Aug 20, 2024Aug 20, 2024

• Pangenome-Graphs-Simulation

  Public
  GNU General Public License v2.0

  •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

• scRNA-seq-data-analysis

  Public
  workshop-material

  Dockerfile

  •

  GNU General Public License v3.0

  •3•2•0•0•Updated Aug 15, 2024Aug 15, 2024

• shell-for-bioinformatics

  Public
  Intermediate-Advanced shell for Bioinformatics

  workshop-material

  HTML

  •

  GNU General Public License v3.0

  •6•4•2•0•Updated Aug 7, 2024Aug 7, 2024

• introduction-to-shell

  Public
  introduction to shell

  workshop-materials

  HTML

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jul 30, 2024Jul 30, 2024

• publicationQualityPlots_ggplot2

  Public
  A short workshop that runs through building plots with ggplot2

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 4, 2024Jul 4, 2024

• GenomicsAotearoa.github.io

  Public
  Code and files for Genomics Aotearoa github.io website

  ga-github-website

  2•2•0•0•Updated Jul 4, 2024Jul 4, 2024

• VariomeGenomeAssembly

  Public
  Shell

  •0•1•0•0•Updated Jul 3, 2024Jul 3, 2024

• Imputation-workshop

  Public
  workshop-material

  Apache License 2.0

  •6•8•0•0•Updated Jun 22, 2024Jun 22, 2024

• long-read-assembly-one-day

  Public
  Long-read assembly workshop modified to run in a single day

  HTML

  •

  GNU General Public License v3.0

  •6•0•0•0•Updated Jun 12, 2024Jun 12, 2024

• introduction-to-nextflow

  Public
  HTML

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jun 4, 2024Jun 4, 2024

• RNA-seq-workshop-on-demand

  Public
  RNA-seq Data Analysis workshop, modified to run on the OnDemand training platform.

  HTML

  •

  Apache License 2.0

  •0•0•0•0•Updated May 21, 2024May 21, 2024

• long-read-microbial-isolate-genomics

  Public
  Sequence processing workflow for samples obtained from microbial isolates sequenced using long-read technology.

  0•0•0•0•Updated May 2, 2024May 2, 2024

• intro-to-containers

  Public
  Introduction to Software containerisation and some of the container platforms such as Apptainer , Docker

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 25, 2024Apr 25, 2024

• Nextflow-Developer-Workshop

  Public
  Best practices for developing your pipelines with Nextflow and nf-core

  CSS

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Mar 19, 2024Mar 19, 2024

• RNA-seq-workshop

  Public
  workshop-material

  HTML

  •

  Apache License 2.0

  •24•18•1•0•Updated Mar 11, 2024Mar 11, 2024

• Nextflow_Workshop

  Public
  A workshop to help you integrate Nextflow in your analysis workflows for reproducible and scalable pipelines.

  workshop-material

  HTML

  •

  GNU General Public License v3.0

  •4•3•0•1•Updated Mar 9, 2024Mar 9, 2024

• Introduction-to-Bash

  Public
  Introduction to the Command Line for Genomics

  Other

  •190•1•0•0•Updated Feb 13, 2024Feb 13, 2024

• nesi-jupyter

  Public
  NeSI Mahuika cluster Jupyter login details

  CSS

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 11, 2024Feb 11, 2024

• AGM-workshop-2023

  Public archive
  HTML

  •

  GNU General Public License v3.0

  •2•1•1•1•Updated Nov 26, 2023Nov 26, 2023

• hts_workshop_mpi

  Public
  Training materials for the 2023 HTS Plant Health and Environment Laboratory workshop

  workshop-material

  HTML

  •3•3•0•0•Updated Nov 20, 2023Nov 20, 2023

• data-management-resources

  Public
  Repo supporting the manuscript 'Journeying towards best practice data management in biodiversity genomics'.

  genomicsresourcesdata-management+ 4fair-principlesdigital-sequence-informationcare-principlesindigenous-data-sovereignty

  HTML

  •

  Creative Commons Attribution 4.0 International

  •0•3•0•0•Updated Oct 25, 2023Oct 25, 2023

• Kakapo

  Public
  Scripts and code for Kākāpō genomic data

  popgenpopulation-geneticshigh-quality-genomes

  Jupyter Notebook

  •1•14•0•0•Updated Sep 4, 2023Sep 4, 2023