Repositories list

• covid_in_wastewater

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

  5•20•0•0•Updated Nov 14, 2024Nov 14, 2024

• Notifiable-Diseases-Annual-Dashboard-

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

  GNU General Public License v3.0

  •1•2•0•0•Updated Jul 3, 2024Jul 3, 2024

• 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

  •112•0•0•0•Updated Aug 7, 2023Aug 7, 2023

• mycosnp-nf

  Public
  CDCgov/mycosnp-nf

  Nextflow

  •

  Apache License 2.0

  •33•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.

  genomicsexome-pipelineillumina+ 7nvidia-gpucohort-analysisgatk4snakemake-pipelinegatk-bestpracticesnvidia-clara-parabrickspipeline

  Python

  •21•31•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 human_genomics_pipeline.

  genomicsvcfbioinformatics-pipeline+ 2annotation-toolsnakemake-pipeline

  Python

  •6•8•5•1•Updated May 30, 2022May 30, 2022

• snakemake_workshop

  Public archive
  Snakemake workshop

  HTML

  •

  Other

  •8•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

  •14•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

  •508•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