add section on CIVET reports
Opened this issue · 1 comments
tavareshugo commented
- 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 commented
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 fromsnakemake
. In theenvironment.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