New implementation of the **CreateSchema** process. This new implementation significantly reduces execution time. It is designed to enable schema creation based on hundreds or thousands of assemblies on a laptop. The schemas generated by the new implementation are fully compatible with previous versions.
Additional changes
- Improved detection of invalid inputs (inputs that do not contain coding sequences (CDSs), that contain invalid sequences/characters, empty files, etc).
- New parameter `--pm` allows users to set Prodigal's execution mode. The `single` mode is the default mode. Use the `meta` mode for input files that have less than 100kbp (e.g.: plasmids, viruses).
- `CreateSchema` accepts a single or several FASTA files with CDSs if the `--CDS` option is included in the command. This option skips the gene prediction step with Prodigal and creates a schema seed based on the CDSs in the input files.
- `AlleleCall` can automatically detect parameter values previously used with a schema. Users only need to provide values for the `-i`, `-g` and `-o` parameters.