Institute of Environmental Science and Research's repositories
human_genomics_pipeline
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
covid_in_wastewater
Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater
nz-sars-cov2-variants
Data on prevalence of variants of concern in Aotearoa New Zealand
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.
POx_POC_pipeline
Point of care species ID by kraken2 ONT read classification for Xaiver platform
GraphPanGenomes_Microbial
Microbial genomics pipeline to build and analyse genome graphs
2019-05-28-DC-ESR-MASC
MASC DC Workshop 28-29 May 2019
GenomicsNarrativeSARSCoV2
A companion document to the genomics data from NZ cases
human_genomics_pipeline_gpu
A GPU accelerated Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using bwa/GATK4.
Notifiable-Diseases-Annual-Dashboard-
This repository is to make Annual Notifiable Disease Dashboard data public.
2019-06-25-DC-ESR-KSC
DC details for ESR KSC workshop
2021-04-13-ESR-R-ecology-lesson
Data Analysis and Visualization in R for Ecologists
abritamr
A pipeline for running AMRfinderPlus and collating results into functional classes
mycosnp-nf
CDCgov/mycosnp-nf
snakemake_workshop
Snakemake workshop
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples