update: refreshing the databases

More and more sequences are uploaded to NCBI database every month. The figure shows the number of viral sequences with complete genome in the title that are submitted every month to NCBI (code).

Code used to create the figure is here

VirMet provides a simple way to update the viral database with the subcommand update as in the example

virmet update --viral n

Similarly, new bacterial sequences can be added as well as fungal. Bacterial and bovine database, since they consist of a single organism, don't need to be updated so often.

Don't forget to index the database again once it has been updated.

Adding sequences manually

By adding the switch --picked file_with_ids users can add sequences by writing their ids in a file, one per line.