Repositories list

• BioinformaticsTrainingProgramme

  Public
  Material for bioinformatics training programme website

  HTML

  •0•0•1•0•Updated Oct 31, 2025Oct 31, 2025

• reproducibility_with_git_and_quarto

  Public
  A two day workshop on reproducibility with Git and Quarto

  CSS

  •

  GNU General Public License v3.0

  •0•1•8•0•Updated Oct 28, 2025Oct 28, 2025

• RNA-seq-data-analysis-workflow

  Public
  A workflow for analysing RNA-seq data, aimed at new users who want to understand the methods available.

  workshop-materials

  CSS

  •

  GNU General Public License v3.0

  •0•0•9•0•Updated Oct 13, 2025Oct 13, 2025

• Introduction-to-R

  Public
  Introduction to R

  workshop-material

  Creative Commons Zero v1.0 Universal

  •2•3•2•0•Updated Oct 12, 2025Oct 12, 2025

• hts_workshop_mpi

  Public
  Training materials for the 2025 HTS Plant Health and Environment Laboratory workshop

  workshop-material

  HTML

  •4•3•0•0•Updated Oct 7, 2025Oct 7, 2025

• 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 Sep 30, 2025Sep 30, 2025

• visualization_day

  Public
  Visualisation is more than just the code used to make a plot.

  workshop-materials

  HTML

  •0•0•3•0•Updated Sep 14, 2025Sep 14, 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•7•0•0•Updated Sep 1, 2025Sep 1, 2025

• Intermediate-R

  Public
  Intermediate R workshop material

  workshop-material

  HTML

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  GNU General Public License v3.0

  •3•4•5•0•Updated Aug 26, 2025Aug 26, 2025

• Hoiho

  Public
  Scripts, Parameters, and Analyses for Hoiho Publication

  1•0•0•0•Updated Aug 11, 2025Aug 11, 2025

• shell-for-bioinformatics

  Public
  Intermediate-Advanced shell for Bioinformatics

  workshop-material

  HTML

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  GNU General Public License v3.0

  •6•5•3•0•Updated Aug 4, 2025Aug 4, 2025

• workflow.DNA_virus_niche_adaptations

  Public
  Python

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  MIT License

  •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

• HPGP-basics

  Public
  Human Pangenome Project basics

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 12, 2025Jun 12, 2025

• microbial_genomics_short_reads

  Public
  Training workshop for microbial genome assembly using short sequencing reads.

  CSS

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 13, 2025May 13, 2025

• nesi-jupyter

  Public
  NeSI Mahuika cluster Jupyter login details

  CSS

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 11, 2025May 11, 2025

• 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•2•0•Updated Mar 3, 2025Mar 3, 2025

• environmental_metagenomics

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

  environmental-metagenomics

  HTML

  •7•12•0•0•Updated Feb 17, 2025Feb 17, 2025

• 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

  •31•66•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

• 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

• introduction-to-shell

  Public
  introduction to shell

  workshop-materials

  HTML

  •

  GNU General Public License v3.0

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

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  GNU General Public License v3.0

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

• RNA-seq-workshop-on-demand

  Public archive
  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

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  GNU General Public License v3.0

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