bioinformatics

GSoC 2022, GA4GH and BioSerDe (pt2)

Google Summer of Code 2022 with GA4GH (pt2)

Gabriel Frank Simonetto, Roman Valls Guimera

Last updated on Oct 9, 2022 4 min read rust, BioSerDe, bioinformatics, serialization

GSoC 2022, GA4GH and BioSerDe

Google Summer of Code 2022 with GA4GH

Gabriel Frank Simonetto, Roman Valls Guimera

Last updated on Oct 11, 2022 6 min read rust, BioSerDe, bioinformatics, serialization

IGV frontend (desktop client) setup

Adding the Amazon provisioning URL to IGV desktop

Roman Valls Guimera

Last updated on Sep 21, 2021 3 min read bioinformatics, infrastructure

GSoC 2021, GA4GH and htsget-rs

Google Summer of Code 2021 with GA4GH: A pure Rust htsget implementation is born

Roman Valls Guimera

Last updated on Nov 15, 2021 5 min read rust, htsget, bioinformatics, infrastructure

Amazon IGV backend setup

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

Andrew Patterson, Roman Valls Guimera

Last updated on Sep 21, 2021 10 min read bioinformatics, infrastructure

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

Last updated on Sep 22, 2021 9 min read bioinformatics

Panel of normals

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

Last updated on Sep 21, 2021 6 min read bioinformatics

Amazon for the Integrative Genomics Viewer (IGV)

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

Roman Valls Guimera

Last updated on Sep 22, 2021 7 min read bioinformatics, infrastructure

BWA-MEM vs Minimap2: WGS somatic variant calling

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

Last updated on Sep 21, 2021 5 min read bioinformatics