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add section on CIVET reports #25

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tavareshugo opened this issue Sep 1, 2022 · 1 comment
Open

add section on CIVET reports #25

tavareshugo opened this issue Sep 1, 2022 · 1 comment
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enhancement New feature or request

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@tavareshugo
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  • See these materials for inspiration
  • I think the data can be downloaded from COG-UK website (see the links at the very bottom of the page)
  • The data it needs are detailed in the CIVET docs (alignment.fasta, metadata.csv, phylogeny.nexus)
@tavareshugo tavareshugo added the enhancement New feature or request label Sep 1, 2022
@tavareshugo
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I need to put these things down in scripts, but for now just documenting it here:

  • Default installation of civet failed, due to an error from snakemake. In the environment.yml they set <=6.8.0, but updating it to 7.16.0 fixed the problem.
  • Downloaded background data from GISAID following these instructions: https://cov-lineages.org/resources/civet/walkthrough.html#background_dataset
  • Ran: civet -bd align_curate -bd-seqs hcov_asia/hcov_asia.fasta -bd-metadata hcov_asia/hcov_asia.tsv --sequence-id-column strain
  • Then the analysis: civet -i report/metadata.csv -f report/consensus.fa -icol sample -idate date -d resources/civet_data -o results/civet -bicol modified_strain

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