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@ESR-NZ PHF Science - New Zealand Institute for Public Health and Forensic Science

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    Repositories list

    25 repositories

    • covid_in_wastewater

      Public
      Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater
      4•22•0•0•Updated Oct 22, 2026Oct 22, 2026

    • Notifiable-Diseases-Annual-Dashboard-

      Public
      This repository is to make Annual Notifiable Disease Dashboard data public.
      GNU General Public License v3.0
      •1•3•0•0•Updated Oct 6, 2026Oct 6, 2026

    • nz-seawater_intrusion_risk_to_2150

      Public
      Random forest model of groundwater table elevation (to 10 km from the nearest coast) relative to sea level under projections of sea level rise and vertical land…
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 7, 2026May 7, 2026

    • nz-sars-cov2-variants

      Public
      Data on prevalence of variants of concern in Aotearoa New Zealand
      5•12•0•0•Updated Feb 22, 2024Feb 22, 2024

    • Training

      Public
      training materials
      0•2•0•0•Updated Sep 11, 2023Sep 11, 2023

    • viralrecon

      Public
      Assembly and intrahost/low-frequency variant calling for viral samples
      Nextflow
      •
      MIT License
      •159•0•0•0•Updated Aug 7, 2023Aug 7, 2023

    • mycosnp-nf

      Public
      CDCgov/mycosnp-nf
      Nextflow
      •
      Apache License 2.0
      •46•0•0•0•Updated Jul 26, 2023Jul 26, 2023

    • human_genomics_pipeline

      Public
      A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
      pipelinegenomicsexome-pipeline
      pipelinegenomicsexome-pipelineilluminanvidia-gpucohort-analysisgatk4snakemake-pipelinegatk-bestpracticesnvidia-clara-parabricks
      Python
      •22•35•1•0•Updated Jan 13, 2023Jan 13, 2023

    • GTW

      Public
      Genomics training week notes and install instructions
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 9, 2022Nov 9, 2022

    • GraphPanGenomes_Microbial

      Public
      Microbial genomics pipeline to build and analyse genome graphs
      Roff
      •
      GNU General Public License v3.0
      •4•3•0•0•Updated Sep 21, 2022Sep 21, 2022

    • vcf_annotation_pipeline

      Public
      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 hu…
      genomicsvcfbioinformatics-pipeline
      genomicsvcfbioinformatics-pipelineannotation-toolsnakemake-pipeline
      Python
      •6•9•5•1•Updated May 30, 2022May 30, 2022

    • snakemake_workshop

      Public archive
      Snakemake workshop
      HTML
      •
      Other
      •9•0•0•0•Updated Apr 2, 2022Apr 2, 2022

    • POx_POC_pipeline

      Public
      Point of care species ID by kraken2 ONT read classification for Xaiver platform
      Python
      •5•5•0•2•Updated Mar 28, 2022Mar 28, 2022

    • NZ_COVID19_Data

      Public
      5•13•2•0•Updated Feb 12, 2022Feb 12, 2022

    • ESR_reporting_template

      Public
      HTML
      •0•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • abritamr

      Public
      A pipeline for running AMRfinderPlus and collating results into functional classes
      Python
      •18•0•0•0•Updated Nov 22, 2021Nov 22, 2021

    • GenomicsNarrativeSARSCoV2

      Public
      A companion document to the genomics data from NZ cases
      Creative Commons Attribution 4.0 International
      •1•1•0•0•Updated Oct 24, 2021Oct 24, 2021

    • NZ_SARS-CoV-2_genomics

      Public
      Shell
      •2•7•0•0•Updated Sep 21, 2021Sep 21, 2021

    • 2021-04-13-ESR

      Public
      Python
      •
      Other
      •2•0•0•0•Updated Apr 12, 2021Apr 12, 2021

    • 2021-04-13-ESR-R-ecology-lesson

      Public
      Data Analysis and Visualization in R for Ecologists
      R
      •
      Other
      •523•0•0•0•Updated Mar 19, 2021Mar 19, 2021

    • 2020-11-24-ESRpython

      Public
      HTML
      •
      Other
      •0•1•0•0•Updated Nov 22, 2020Nov 22, 2020

    • human_genomics_pipeline_gpu

      Public archive
      A GPU accelerated Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using bwa/GATK4.
      Python
      •2•1•0•0•Updated Sep 9, 2020Sep 9, 2020

    • opentrons_protocols

      Public
      Python
      •1•0•0•0•Updated Jun 9, 2020Jun 9, 2020

    • 2019-06-25-DC-ESR-KSC

      Public
      DC details for ESR KSC workshop
      Python
      •
      Other
      •0•0•0•0•Updated Jun 19, 2019Jun 19, 2019

    • 2019-05-28-DC-ESR-MASC

      Public
      MASC DC Workshop 28-29 May 2019
      Python
      •
      Other
      •0•2•0•0•Updated May 19, 2019May 19, 2019
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