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Revision as of 09:24, 25 April 2020 by Jaruga (talk | contribs)

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.


Focusing projects

We list up the COVID-19 analysis focusing projects. This is a a top-down approach to find the areas.

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 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