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=== nf-core === | === nf-core === | ||
nf-core is a collection of Nextflow | [https://nf-co.re/ nf-core] is a collection of analysis pipelines built using [https://www.nextflow.io/ Nextflow]. We refer it to see the actual analysis workflow to identify the used bio tools projects. Podman is supported as one of the container workflows according to [https://www.nextflow.io/docs/edge/podman.html this page]. | ||
Talking people in the project, nf-core/nanoseq, nf-core/artic and nf-core/viralrecon are primarily important. | Talking people in the project, nf-core/nanoseq, nf-core/artic and nf-core/viralrecon are primarily important. | ||
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* Single-cell analysis: [https://nf-co.re/scrnaseq nf-core/scrnaseq], [https://nf-co.re/smartseq2 nf-core/smartseq2] | * Single-cell analysis: [https://nf-co.re/scrnaseq nf-core/scrnaseq], [https://nf-co.re/smartseq2 nf-core/smartseq2] | ||
* Whole-genome sequencing analysis: [https://nf-co.re/sarek nf-core/sarek] | * Whole-genome sequencing analysis: [https://nf-co.re/sarek nf-core/sarek] | ||
* | * Meta-genomics analysis: [https://nf-co.re/mag nf-core/mag] | ||
* Investigations into the immune response: [https://nf-co.re/bcellmagic nf-core/bcellmagic] | * Investigations into the immune response: [https://nf-co.re/bcellmagic nf-core/bcellmagic] | ||
Revision as of 14:10, 24 April 2020
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
Projects used in COVID-19
We list up the projects used in the COVID-19. 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 it to see the actual analysis workflow to identify the used bio tools projects. Podman is supported as one of the container workflows according to this page.
Talking people in the project, nf-core/nanoseq, nf-core/artic and nf-core/viralrecon are primarily important.
- nf-core/nanoseq
- nf-core/artic (in development)
- nf-core/viralrecon (in development)
Following pipelines could be certainly relevant.
- Single-cell analysis: nf-core/scrnaseq, nf-core/smartseq2
- Whole-genome sequencing analysis: nf-core/sarek
- Meta-genomics analysis: nf-core/mag
- Investigations into the immune response: nf-core/bcellmagic
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.
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 [https://opensource.com/article/20/3/open-hardware-covid19
this article], there are open source hardware projects related to
- Ventilator
- Llabware, consumables, reagents
- Polymerase chain reaction (PCR) device