mmlong2: v1.1.0

• 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

mmlong2: v0.9.2

• Dependency updates, including Medaka models for 5 kHz Nanopore simplex data and GTDB r214 for MAG taxonomy
• Several stability improvements when re-running the workflow after a crash has occurred

mmlong2: v0.9.0

• Pipeline upgrade from shell script to Snakemake workflow
• Dependency switch from local installations to singularity container for improved reproducibility and distribution
• Rework of the binning stage to improve MAG recovery

mmlong2 v0.0.4

• Added MiDAS 16S-based taxonomy for MAGs
• Updated CheckM2 to v1.0.0
• Output directory name will now be included in the MAG names
• Minor compatibility fixes

Initial release

mmlong2: the early, in-house bash script days