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Input background data

civet summarises information around a set of sequences of interest. It relies on the user providing a background tree, alignment and metadata file.

The data files civet looks for are:

cog_global_2020-XX-YY_alignment.fasta
cog_global_2020-XX-YY_metadata.csv
cog_global_2020-XX-YY_tree.nexus

--CLIMB

For SARS-CoV-2, this data is hosted on CLIMB as part of COG-UK. To run civet on CLIMB with the latest data, either

  1. Use the --CLIMB flag or
  2. Specify CLIMB: True in the config.yaml file

This provides civet with the path to the latest data on CLIMB and allows the user to access adm2 information.

-r / --remote

Alternatively, run civet remotely from CLIMB with

  1. The -r / --remote flag or
  2. By adding remote: True to the config file.

If SSH keys are configured, simply run:

civet -i input.csv -r

Otherwise, provide a climb username with -uun / --username:

civet -i input.csv -r -uun climb-covid19-smithj

Notes:

  • This data will access a version of the COG-UK data that is publically available (does not contain adm2 information)
  • To access CLIMB in this way, you must have a valid COG-UK CLIMB username and be in the UK

By default, the data will be pulled down to a directory called civet-cat in the current working directory.

-d / --datadir

The user can specify a custom background data directory with the -d / --datadir flag.

This can be used with the remote option to rsync to an alternative location or without the without the remote flag, civet can just accept the data in that directory as input background data.

This can also be run on CLIMB without the --CLIMB flag to specify an older version of the dataset.

civet -i input.csv -d path/to/data_directory

--background-tree

By default, civet will look for a newick file in the data directory to use as the tree. To provide a custom tree file, use

  1. the --background-tree flag or
  2. add background_tree: path/to/tree.newick to the config file

--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

  1. the --background-sequences flag or
  2. add background_tree: path/to/sequences.fasta to the config file

--background-metadata

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

  1. the --background-metadata flag or
  2. add background_metadata: path/to/metadata.csv to the config file

Background metadata requirements

The following fields must be always present in this background metadata, or civet will not run:

  • sequence_name containing names of every sequence
  • country containing the country of sampling
  • A field to match the input data with containing COG IDs. The default header for this column is set to central_sample_id, but this can be changed by altering the --data-column argument
  • A date column containing the date of sampling. The default header for this column is set to sample_date, but can be changed by altering the --database-sample-date-column argument.

The other fields depend on what you have supplied as optional in the report:

  • node_summary: if you have altered this argument, the column header in the background metadata that this has been set to must be supplied.
  • If the --local-lineages analysis is being undertaken, adm2 must be provided.

Some data can be provided in either the query csv or the background metadata:

  • Any field you include in --table-fields, --label-fields or --tree-fields.
  • If the default options for the --colour-by argument are used, adm1 must be provided in either the background metadata or the query csv.
  • If the default options for --table-fields argument are used, uk_lineage, lineage, phylotype must be included in the background metadata or the query csv.

Next: Usage