This is the GitHub pages site for Genomics Aotearoa, a collaborative research platform for genomics and bioinformatics. The repositories here relate to our in-progress software development and training projects.

If you are interested in learning more about Genomics Aotearoa, please visit our official website at:

https://www.genomics-aotearoa.org.nz/

Projects with public repositories:

General

Available repositories:

• Methods and Musings: contributions from Genomics Aotearoa team members.

Cancer genomics

• Genomic translational oncology
• Cell-free genomics

These projects relate to the development and deployment of data analysis pipelines for processing cancer genomics data. Available repositories:

• cancer-seq-pipeline: bpipe-based pipeline for processing cancer genomics data in fastq format through to annotated variants in a simple report.
• bioinformatics-containers: Docker containers used by cancer-seq-pipeline.
• dbNSFP_build: Docker container for script to download dbNSFP ‘database’ and wrangle it into a format suitable for pipeline annotation process.
• running_smcounter: Notes on getting the qiaseq-dna / smcounter pipeline/workflow up and running with singularity. Created as a regular repo, since organistations can’t have gists.

Bioinformatics training

• Bioinformatics capability

This project relates to the delivery of hands-on bioinformatics training workshops across New Zealand. Available repositories:

• GenomicsAotearoa.github.io - the repository for this website.
• 2019-09-19-ESR - Data Carpentry Genomics repository for upcoming training event at ESR in Porirua.
• cloudsforresearch - A guide to getting started in the cloud.