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@ESR-NZ

Institute of Environmental Science and Research

ESR is New Zealand’s Crown Research Institute that specialises in science relating to people and communities.

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  1. human_genomics_pipeline 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.

    Python 31 21

  2. covid_in_wastewater covid_in_wastewater Public

    Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater

    20 5

  3. NZ_COVID19_Data NZ_COVID19_Data Public

    13 5

  4. nz-sars-cov2-variants nz-sars-cov2-variants Public

    Data on prevalence of variants of concern in Aotearoa New Zealand

    11 5

  5. vcf_annotation_pipeline 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 human_genomics_pipeline.

    Python 8 6

  6. NZ_SARS-CoV-2_genomics NZ_SARS-CoV-2_genomics Public

    Shell 6 2

Repositories

Showing 10 of 24 repositories
  • covid_in_wastewater Public

    Quantitative data about how much SARS-CoV2 virus is found in New Zealand's wastewater

    ESR-NZ/covid_in_wastewater’s past year of commit activity
    20 5 0 0 Updated Nov 22, 2024
  • Notifiable-Diseases-Annual-Dashboard- Public

    This repository is to make Annual Notifiable Disease Dashboard data public.

    ESR-NZ/Notifiable-Diseases-Annual-Dashboard-’s past year of commit activity
    2 GPL-3.0 1 0 0 Updated Jul 3, 2024
  • nz-sars-cov2-variants Public

    Data on prevalence of variants of concern in Aotearoa New Zealand

    ESR-NZ/nz-sars-cov2-variants’s past year of commit activity
    11 5 0 0 Updated Feb 22, 2024
  • Training Public

    training materials

    ESR-NZ/Training’s past year of commit activity
    2 0 0 0 Updated Sep 11, 2023
  • viralrecon Public Forked from nf-core/viralrecon

    Assembly and intrahost/low-frequency variant calling for viral samples

    ESR-NZ/viralrecon’s past year of commit activity
    Nextflow 0 MIT 113 0 0 Updated Aug 7, 2023
  • mycosnp-nf Public Forked from CDCgov/mycosnp-nf

    CDCgov/mycosnp-nf

    ESR-NZ/mycosnp-nf’s past year of commit activity
    Nextflow 0 Apache-2.0 33 0 0 Updated Jul 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.

    ESR-NZ/human_genomics_pipeline’s past year of commit activity
    Python 31 21 1 0 Updated Jan 13, 2023
  • GTW Public

    Genomics training week notes and install instructions

    ESR-NZ/GTW’s past year of commit activity
    0 GPL-3.0 0 0 0 Updated Nov 9, 2022
  • GraphPanGenomes_Microbial Public

    Microbial genomics pipeline to build and analyse genome graphs

    ESR-NZ/GraphPanGenomes_Microbial’s past year of commit activity
    Roff 3 GPL-3.0 4 0 0 Updated Sep 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 human_genomics_pipeline.

    ESR-NZ/vcf_annotation_pipeline’s past year of commit activity
    Python 8 6 5 1 Updated May 30, 2022
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