- Multiple dependency updates and internal stability improvements
- Expanded workflow usage options
- Medaka and GraphMB are now optional
- Added option to run dependencies from pre-defined Conda environments
- Added an optional MetaMDBG assembler for PacBio HiFi reads
- Added automated database installation
- Added Longshot as variant caller for Nanopore and PacBio modes
- Reworked tRNA and rRNA counting to improve assessment of archaeal genomes