COVID-19 analysis pipelines

Question

[konstantinkul]

Hi all,

Could you please suggest the most highly cited, user-friendly, reproducible, and free pipelines from git-hub repositories for COVID-19 data analysis. The input files should be paired-end fastq files (Illumina) or fasta file from assembled reads, and the output should be the consensus sequence, VCF file with mutations, and the table with interpretation. It will be great if there is some minimal database with the interpretation of a particular list of SNPs. I will be thankful for any suggestions!

Answer 1

[GenoMax]

See: SARS Cov2 NGS data analysis pipeline
https://github.com/nf-core/viralrecon
https://docs.nextstrain.org/en/latest/guides/index.html

[konstantinkul]

Thank you so much!