SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly

[thomasbtf]

Hello SIGNAL Team,

I am from the University Hospital Essen, Germany, and we work extensively with SARS-CoV-2 in our research. We have also developed a SARS-CoV-2 workflow. In preparation for the publication of our workflow, we have looked at several other SARS-CoV-2 related workflows, including your work. We will present this review in the publication and want to ensure that your work is represented as accurately as possible.

Moreover, there is currently little to no current overview of SARS-CoV-2 related workflows. Therefore, we have decided to make the above comparison publicly available via this GitHub repository. It contains a table with an overview of the functions of different SARS-CoV-2 workflows and the tools used to implement these functions.

We would like to give you the opportunity to correct any misunderstandings on our side. Please take a moment to make sure we are not misrepresenting your work or leaving out important parts of it by taking a look at this overview table. If you feel that something is missing or misrepresented, please feel free to give us feedback by contributing directly to the repository.

Thank you very much!

cc @alethomas

[fmaguire]

Hi @thomasbtf,

Thanks for reaching out!

I submitted a PR with some modifications to the SIGNAL summary: IKIM-Essen/sars-cov-2-workflow-comparison@main...fmaguire:patch-1

PHA4GE has also gathered some information about bioinformatics resources for SARS-CoV-2 that may be useful to your efforts! https://github.com/pha4ge/pipeline-resources/blob/main/docs/bioinfo-solutions.md

[jaleezyy]

Hi @thomasbtf,

Taking a look at @fmaguire's patch, I agree with his changes! I would propose the re-addition of iVar into the consensus and variant calling sections, given both are still supported with the latest version of SIGNAL, although FreeBayes is prioritized.

PR: IKIM-Essen/sars-cov-2-workflow-comparison@main...jaleezyy:patch-1