civet v2.1.2

Release notes

• Updated release
• Now looks for newick tree on CLIMB
• Minor bug fixes

civet v2.1.1

Fixed git merging errors present in v2.1

civet v2.1

Adm2 cleaning has been removed from mapping scripts, unless old background data is used.
Added QC functions to detect uncleaned Adm2, and will also accept appropriate ambiguity codes.
Docs updated to provide more information on what constitutes an appropriate adm2 region.

civet v2.0.2

Fixing tree numbering bug for trees which are too large

civet v2.0.1

Bug fix in the label_fields option

civet v2.0

civet 2.0

Full details of new features in civet can be found at cog-uk.github.io/civet

Release notes

• civet now accepts an -o / --output-prefix option that gives the stem of the time-stamped directory and the name of the output report file
• civet no longer has positional arguments, rather the input can be given with -i / --input. Valid inputs are a csv file, a comma-separated string of COG-IDs or a yaml config file.

civet -i input.csv
civet -i EDB001,EDB002
civet -i config.yaml

• The config file (yaml format) can be used to run elaborate analyses without having to specify all options on the command line (details here)
• civet now has a --safety-level that configures the level of anonymity in the report (details here)
• Custom background metadata can be provided via --background-metadata with additional metadata fields.
• Running on climb with (--CLIMB) gives the user access to adm2 information, whereas running with the -r / --remote flag only uses publically available data
• The report can now have custom free text specified in the config file, such as custom title, introduction and conclusions. Sections to include in the report can now be configured including barcharts, snipit graphs, appendix and maps
• The tables are now customisable to show fields of interest with --table-fields and --include-snp-table
• Queries can now be defined by matching criteria in the COG database, rather than specifying IDs explicitly, with -fm / --from-metadata. The search matches one or more <column_name>=<value> pairs, or date range with sample_date=<date1>:<date2>.
  Example, to run a report on sequences from Edinburgh in September:

civet --from-metadata adm2=Edinburgh sample_date=2020-09-01:2020-10-01

• --protect can be used to save certain sequences from collapse in the local trees, matched with the same format as --from-metadata, these are distinct from queries as they will not appear in the snipit graphs
• Output now includes the following: (full details here)

civet_metadata.csv # combined metadata on all queries and sequences that appear in the trees
report directory (markdown and html format civet report and associated figures)
catchment_trees # uncollapsed trees
local_trees # collapsed trees with any sequences in `--fasta` added in
final config.yaml file