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    24 repositories

    • covid_in_wastewater

      Public
      Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater
      4•21•0•0•Updated Apr 10, 2026Apr 10, 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 Nov 2, 2025Nov 2, 2025

    • nz-sars-cov2-variants

      Public
      Data on prevalence of variants of concern in Aotearoa New Zealand
      5•11•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
      •148•0•0•0•Updated Aug 7, 2023Aug 7, 2023

    • mycosnp-nf

      Public
      CDCgov/mycosnp-nf
      Nextflow
      •
      Apache License 2.0
      •44•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•34•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•8•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•6•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
      •517•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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