From Fedora Project Wiki

 
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== Analysis ==
 
== Analysis ==
  
=== Focusing projects
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=== Focusing projects ===
  
 
We list up the COVID-19 analysis focusing projects. This is a a top-down approach to find the areas.
 
We list up the COVID-19 analysis focusing projects. This is a a top-down approach to find the areas.
  
* [https://github.com/virtual-biohackathons/covid-19-bh20 COVID19 Virtual Biohackathon 2020]: [https://github.com/virtual-biohackathons/covid-19-bh20/wiki Wiki] [https://github.com/virtual-biohackathons/covid-19-bh20/wiki Home Learning], [https://www.youtube.com/watch?v=x-QTP5Z_WIU Kick-off meeting video], [https://www.youtube.com/watch?v=g5cQk8jIMwo Wrap-up meeting video].
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* [https://github.com/virtual-biohackathons/covid-19-bh20 COVID19 Virtual Biohackathon 2020]: [https://github.com/virtual-biohackathons/covid-19-bh20/wiki Wiki], [https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Home-Learning Home Learning], [https://www.youtube.com/watch?v=x-QTP5Z_WIU Kick-off meeting video], [https://www.youtube.com/watch?v=g5cQk8jIMwo Wrap-up meeting video].
 
* [https://www.codevscovid19.org/ CodeVsCovid19]
 
* [https://www.codevscovid19.org/ CodeVsCovid19]
  
== Projects used in COVID-19 ==
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=== Bio tools used in COVID-19 analysis ===
  
We list up the projects used in the COVID-19. This is a bottom-up approach to find the areas.
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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 ===
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==== nf-core ====
  
[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].
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[https://nf-co.re/ nf-core] is a collection of analysis pipelines built using [https://www.nextflow.io/ Nextflow]. We refer the pipelines to look into the actual analysis workflows to identify the used bio tools projects.
  
Talking people in the project, nf-core/nanoseq, nf-core/artic and nf-core/viralrecon are primarily important.
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Nextflow is the workflow software such as [https://openwdl.org/ Workflow Description Language (WDL)] and [https://www.commonwl.org/ Common Workflow Language (CWL)]. The Podman container workflow is supported by Nextflow according to [https://www.nextflow.io/docs/edge/podman.html this page].
  
* [https://nf-co.re/nanoseq nf-core/nanoseq]
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{| class="wikitable"
* [https://nf-co.re/artic nf-core/artic] (in development)
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|-
* [https://nf-co.re/viralrecon nf-core/viralrecon] (in development)
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! Pipeline !! Description !! Relevant level !! Status
 +
|-
 +
| [https://nf-co.re/nanoseq nf-core/nanoseq] || Nanopore DNA/RNA sequencing analysis || Essential (High) || Stable
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|-
 +
| [https://nf-co.re/artic nf-core/artic] || COVID-19 sequencing analysis. Reimplementation of [https://github.com/artic-network/fieldbioinformatics the ARTIC field bioinformatics pipeline] || Essential (High) || In development
 +
|-
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| [https://nf-co.re/viralrecon nf-core/viralrecon] || COVID-19 sequencing anaysis. Variant calling for viral samples. || Essential (High) || In development
 +
|-
 +
| [https://nf-co.re/scrnaseq nf-core/scrnaseq] || Single-cell analysis || Certainly relevant (Middle) || Stable
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|-
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| [https://nf-co.re/smartseq2 nf-core/smartseq2] || Single-cell analysis || Certainly relevant (Middle) || Stable
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|-
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| [https://nf-co.re/sarek nf-core/sarek] || Whole-genome sequencing analysis || Certainly relevant (Middle) || Stable
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|-
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| [https://nf-co.re/mag nf-core/mag] || Meta-genomics analysis || Certainly relevant (Middle) || Stable
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|-
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| [https://nf-co.re/bcellmagic nf-core/bcellmagic] || Investigations into the immune response || Certainly relevant (Middle) || Stable
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|}
  
Following pipelines could be certainly relevant.
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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.
  
* Single-cell analysis: [https://nf-co.re/scrnaseq nf-core/scrnaseq], [https://nf-co.re/smartseq2 nf-core/smartseq2]
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This information comes from the hearing in the nf-core community.
* 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]
 
 
 
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 ===
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==== Packages list ====
  
 
* [https://blends.debian.org/med/tasks/covid-19 Debian Med COVID-19 packages]
 
* [https://blends.debian.org/med/tasks/covid-19 Debian Med COVID-19 packages]
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== Open Hardware ==
 
== Open Hardware ==
  
According to [https://opensource.com/article/20/3/open-hardware-covid19
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According to [https://opensource.com/article/20/3/open-hardware-covid19 this article], there are open source hardware projects related to
this article], there are open source hardware projects related to
 
  
 
* Ventilator
 
* Ventilator
 
* Llabware, consumables, reagents
 
* Llabware, consumables, reagents
 
* Polymerase chain reaction (PCR) device
 
* Polymerase chain reaction (PCR) device

Latest revision as of 17:57, 17 May 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.

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