AWS Rust Lambdas and Bioinformatics

Google Summer of Code 2021 with the Global Alliance for Genomics and Health, implementing htsget in Rust, Noodles and AWS Lambdas

About Us

With a growing need for data management, analysis and research computing support – in particular due to the unprecedented growth of sequencing data – researchers and clinicians will benefit from community-driven, reusable approaches to process, analyse and aggregate large-scale sequencing data. Led by Associate Professor Oliver Hofmann, the Genomics Platform Group is developing, testing, and applying accredited bioinformatics workflows to patient data and large scale research projects, evaluating new technologies at a rapid pace.

Amazon IGV backend setup

Setting up a secure Amazon Cognito and S3 backend for IGV desktop

The first Victorian Cancer Bioinformatics Symposium

On Friday, August 16th 2019, the [Victorian Cancer Bioinformatics Symposium]( aims to bring together those with an interest in the application of bioinformatics in cancer research and clinical practice.

Oncoviral integration in cervical never-responder

We are detecting sites of HPV18 oncovirus integration into the human genome, and investigating the mechanism it facilitated cervical cancer progression

Panel of normals

Building a panel of unrelated normals to filter somatic variant calls from artefacts and germline leakage.

Amazon for the Integrative Genomics Viewer (IGV)

On expanding the Broad's Integrative Genomics Viewer (IGV) to read input directly from AWS S3.

BWA-MEM vs Minimap2: WGS somatic variant calling

We evaluate differences between bwa-mem and minimap2-aligned reads for somatic variant calling.