The following are links to Genomics Aotearoa GitHub repositories that implement specific analysis workflows.
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environmental_metagenomics - A quick workflow to get researchers started with the bioinformatic pipeline used in the Environmental Metagenomics program.
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long-read-microbial-isolate-genomics - Sequence processing workflow for samples obtained from microbial isolates sequenced using long-read technology.
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High-quality-genomes - This repository aims to hosting workflows/codes that have been developed for GA high-quality-genome projects.
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data-management-resources - Repo supporting the manuscript 'Journeying towards best practice data management in biodiversity genomics'.
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Kakapo - Scripts and code for Kākāpō genomic data
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BMSB-popgenomics - Population genomic analysis of the brown marmorated stink bug, Halyomorpha halys for the GA Invasomics project
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GraphPanGenomes_Microbial - Microbial genomics pipeline to build and analyse genome graphs
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vcf_annotation_pipeline - A Snakemake workflow to filter, annotate and prepare variant call format (VCF) data for scout using GATK4, SnpSift, VEP and genmod. Designed to be used after human_genomics_pipeline.
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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.
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He Kākano - The Aotearoa Variome Resource
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Rakeiora: genomic medicine pathfinder project