This page is Fedora Medical SIG's COVID-19 page.
As the COVID-19 is of many people's interest, the page is created for people who want to contribute or do RPM packaging.
Analysis
Focusing projects
We list up the COVID-19 analysis focusing projects. This is a a top-down approach to find the areas.
- COVID19 Virtual Biohackathon 2020: Wiki, Home Learning, Kick-off meeting video, Wrap-up meeting video.
- CodeVsCovid19
Bio tools used in COVID-19 analysis
We list up the bio tools projects used in the COVID-19 analysis. This is a bottom-up approach to find the areas.
nf-core
nf-core is a collection of analysis pipelines built using Nextflow. We refer the pipelines to look into the actual analysis workflows to identify the used bio tools projects.
Nextflow is the workflow software such as Workflow Description Language (WDL) and Common Workflow Language (CWL). The Podman container workflow is supported by Nextflow according to this page.
| Pipeline | Description | Relevant level | Status |
|---|---|---|---|
| nf-core/nanoseq | Nanopore DNA/RNA sequencing analysis | Essential (High) | Stable |
| nf-core/artic | COVID-19 sequencing analysis. Reimplementation of the ARTIC field bioinformatics pipeline | Essential (High) | In development |
| nf-core/viralrecon | COVID-19 sequencing anaysis. Variant calling for viral samples. | Essential (High) | In development |
| nf-core/scrnaseq | Single-cell analysis | Certainly relevant (Middle) | Stable |
| nf-core/smartseq2 | Single-cell analysis | Certainly relevant (Middle) | Stable |
| nf-core/sarek | Whole-genome sequencing analysis | Certainly relevant (Middle) | Stable |
| nf-core/mag | Meta-genomics analysis | Certainly relevant (Middle) | Stable |
| nf-core/bcellmagic | Investigations into the immune response | Certainly relevant (Middle) | Stable |
As almost any molecular biology technique can be used to look into some aspect of COVID-19, virtually all the nf-core pipeline can be relevant.
This information comes from the hearing in the nf-core community.
Packages list
Distributed Computing
The distributed computing projects are to enable people to help COVID-19 analysis by their computer resources.
Open Hardware
According to this article, there are open source hardware projects related to
- Ventilator
- Llabware, consumables, reagents
- Polymerase chain reaction (PCR) device