COVID-19 analysis pipelines · Biostar

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COVID-19 analysis pipelines

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!

dna-seq covid-19 pipeline illumina

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updated 5.5 years ago by GenoMax

• written 5.5 years ago by konstantinkul

Does it need a function to submit to Nature right away or is that optional?

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written 5.5 years ago by ATpoint

)))) it is not necessary )

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written 5.5 years ago by konstantinkul

1 answer

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

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written 5.5 years ago by GenoMax

Thank you so much!

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written 5.5 years ago by konstantinkul

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