SARS Cov2 NGS data analysis pipeline

Question

[arash.iranzadeh1980]

Hi,

Anyone can introduce tools (pipelines) that are suitable for analysis of the coronavirus NGS data (Illumina MiSeq platform) including quality control, phylogeny and variant calling?

Thanks!

[GenoMax]

Past threads: Protocol for genome assembly of Sars-cov-2 sequences
introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data

[arash.iranzadeh1980]

Thank you very much for the link and tutorial!

Answer 1

[Akshay Zawar]

Hi,

You can refer to this link: https://github.com/CDCgov/SARS-CoV-2_Sequencing#sequencing

This GitHub page from the CDC provide in-depth information on NGS practices and Bioinformatics approaches to sequence Sars-Cov-2.

[arash.iranzadeh1980]

Many thanks! Seems useful.

Answer 2

[trausch]

We recently set-up an NGS data analysis pipeline for short-read SARS-CoV-2 sequencing.

[arash.iranzadeh1980]

Great, Thank you so much!