genomicsaotearoa Goto Github PK

advanced-shell-for-bioinformatics

advanced-shell-for-bioinformatics

agm-workshop-2023

bioinformatics-containers

Docker containers used by cancer-seq-pipeline.

bmsb-popgenomics

Population genomic analysis of the brown marmorated stink bug, Halyomorpha halys for the GA Invasomics project

cancer-seq-pipeline

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

clinical_genomics

Workflows relating to the GA clinical genomics project

cloudsforresearch

A guide to getting started in the cloud

communications

data-management-resources

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

dbnsfp_build

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

diagnostics_exome_reporting

Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.

environmental_metagenomics

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

ewas_dap

EWAS Data Analysis

flye

De novo assembler for single molecule sequencing reads using repeat graphs

ga-good-practice

ga-workshop-tutorial

ga_community_pages

Pages for good practice discussion, examples and more

gene_regulatory_networks_simulation_workshop

genome-assembly-workshop

genomic-markers-of-invasiveness

Analysis of genomic markers in invasive and non-invasive species genomes for the GA Invasomics project.

genomicsaotearoa.github.io

Code and files for Genomics Aotearoa github.io website

graphpangenomes_microbial

Microbial genomics pipeline to build and analyse genome graphs

hi-c-workshop

high-quality-genomes

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

hts_workshop_mpi

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

human_genomics_pipeline

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

imputation-workshop

indigidataaotearoa-introtoshell

indigidataaotearoa_introtor

Intro to R coding block for Indigidata Aotearoa

intermediate-r