GenomicsAotearoa/GA_community_pages

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GenomicsAotearoa/GA_community_pages

GenomicsAotearoa

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Pages for good practice discussion, examples and more

metagenomics_summer_school

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

RNA-seq-workshop

Kakapo

Scripts and code for Kākāpō genomic data

Jupyter Notebook

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.

Imputation-workshop

Gene_Regulatory_Networks_Simulation_Workshop

High-quality-genomes

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

Pangenome-Graphs-Workshop

This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.

long-read-assembly

Long-read assembly workshop

Reproducible_Bioinformatics

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.

Hi-C-workshop

Introduction-to-R

Introduction to R

cancer-seq-pipeline

Bpipe-based pipeline for processing cancer genomics data in fastq format through to annotated variants in a simple report.

EWAS_DAP

EWAS Data Analysis

clinical_genomics

Workflows relating to the GA clinical genomics project

workshops-nz

Intermediate-R

scRNA-seq-data-analysis

IndigiDataAotearoa-IntroToShell

cloudsforresearch

A guide to getting started in the cloud

Genome-Assembly-Workshop

advanced-shell-for-bioinformatics

advanced-shell-for-bioinformatics

Singularity

bioinformatics-containers

Docker containers used by cancer-seq-pipeline.

dbNSFP_build

Docker container to download dbNSFP 'database' and wrangle it into a format suitable for pipeline annotation process

GenomicsAotearoa.github.io

Code and files for Genomics Aotearoa github.io website

AGM-workshop-2023

VariomeGenomeAssembly

IndigiDataAotearoa_IntroToR

Intro to R coding block for Indigidata Aotearoa