PHF Science - New Zealand Institute for Public Health and Forensic Science

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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 35 22

2. covid_in_wastewater covid_in_wastewater Public

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

   22 4

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

   12 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 9 6

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

   Shell 7 2