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    • Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater
      42100Updated Apr 10, 2026Apr 10, 2026
    • This repository is to make Annual Notifiable Disease Dashboard data public.
      GNU General Public License v3.0
      1300Updated Nov 2, 2025Nov 2, 2025
    • Data on prevalence of variants of concern in Aotearoa New Zealand
      51100Updated Feb 22, 2024Feb 22, 2024
    • Training

      Public
      training materials
      0200Updated Sep 11, 2023Sep 11, 2023
    • Assembly and intrahost/low-frequency variant calling for viral samples
      Nextflow
      MIT License
      148000Updated Aug 7, 2023Aug 7, 2023
    • CDCgov/mycosnp-nf
      Nextflow
      Apache License 2.0
      44000Updated Jul 26, 2023Jul 26, 2023
    • A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
      Python
      223410Updated Jan 13, 2023Jan 13, 2023
    • GTW

      Public
      Genomics training week notes and install instructions
      GNU General Public License v3.0
      0000Updated Nov 9, 2022Nov 9, 2022
    • Microbial genomics pipeline to build and analyse genome graphs
      Roff
      GNU General Public License v3.0
      4300Updated Sep 21, 2022Sep 21, 2022
    • 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…
      Python
      6851Updated May 30, 2022May 30, 2022
    • snakemake_workshop

      Public archive
      Snakemake workshop
      HTML
      Other
      9000Updated Apr 2, 2022Apr 2, 2022
    • Point of care species ID by kraken2 ONT read classification for Xaiver platform
      Python
      5502Updated Mar 28, 2022Mar 28, 2022
    • 51320Updated Feb 12, 2022Feb 12, 2022
    • HTML
      0000Updated Dec 9, 2021Dec 9, 2021
    • abritamr

      Public
      A pipeline for running AMRfinderPlus and collating results into functional classes
      Python
      18000Updated Nov 22, 2021Nov 22, 2021
    • A companion document to the genomics data from NZ cases
      Creative Commons Attribution 4.0 International
      1100Updated Oct 24, 2021Oct 24, 2021
    • Shell
      2600Updated Sep 21, 2021Sep 21, 2021
    • Python
      Other
      2000Updated Apr 12, 2021Apr 12, 2021
    • Data Analysis and Visualization in R for Ecologists
      R
      Other
      517000Updated Mar 19, 2021Mar 19, 2021
    • HTML
      Other
      0100Updated Nov 22, 2020Nov 22, 2020
    • A GPU accelerated Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using bwa/GATK4.
      Python
      2100Updated Sep 9, 2020Sep 9, 2020
    • Python
      1000Updated Jun 9, 2020Jun 9, 2020
    • DC details for ESR KSC workshop
      Python
      Other
      0000Updated Jun 19, 2019Jun 19, 2019
    • MASC DC Workshop 28-29 May 2019
      Python
      Other
      0200Updated May 19, 2019May 19, 2019
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