civet summarises information around a set of sequences of interest. It relies on the user providing an alignment and metadata file, and an optional SNP file for speed-ups.

By default, civet will search for an environment variable CIVET_DATADIR and use this to find the background data. This can be overwritten by providing the `-d/--datadir` flag or by specifying `datadir` in the optional civet config file.

Background data files

A metadata.csv file. (Required)

An alignment fasta file. (Required)

Optionally, a mutations.csv file. (Optional)

The records in each file should correspond 1:1 in the fasta file, metadata file and SNP file.

civet will look for these files in the `-d/--datadir` specified, or alternatively they can be provided with specific flags/ config arguments:

-bseq/--background-sequences

By default, civet will look for a fasta file in the data directory to use as the background sequence dataset. To provide a custom fasta file, use

the ``-bf/--background-sequences`` flag

add `background_sequences: .fasta` to the config file

-bm/--background-metadata

By default, civet will look for a csv containing background data in the data directory. However, to provide custom background data, use

the ``--background-metadata`` flag

add `background_metadata: .csv` to the config file

For more information on how to configure options connected to background metadata columns, see Background column configuration

-bsnp/--background-snps

By default, civet will look for a csv containing background SNPs in the data directory. However, to provide custom background SNPs, use

the ``--background-snps`` flag

add `background_snps: .csv` to the config file

To generate the SNP file as a time-saver if you’re planning on running multiple civet reports on the same dataset, run

gofasta updown list -q .fasta

to generate the SNP data file for the background data.

--background-data-checks

Run checks on cusom background data files Default: False

-bt/--background-tree

coming soon