MIntO 2.0.0 first beta version

MIntO has gone through major improvements. We have gone straight to version 2.0.0 as the directory structures and configuration field names have changed dramatically. This means that old configuration files are not compatible with version 2.0.0 onwards.

Improvements:

• Much faster due to several optimizations under the hood.
• More user-friendly:
  • Installation is even more simplified.
  • Example script to run the entire tutorial, which we have tested extensively.

Software version upgrades:

• MetaPhlAn updated to v4.0.6.
• mOTUs updated to v3.0.3.
• Genome binner updated to AVAMB v4.1.1.
• Genome completeness check updated to CheckM2 v1.0.1.

Newly supported features:

• Taxonomic profiling, assembly and MAG generation now enabled for metaT.
• Taxonomy profiles are tagged with profiler version, so that upgrading a profiler does not overwrite existing results.
• External reference genomes can be given as just .fna files and MIntO will perform genome annotation.
• Replicate samples can be merged for post analysis.
• MAGs are made using AVAMB with a combination of VAE and AAE, as recommended by AVAMB developers.
• VAMB GPU mode can be enabled if the server installing via dependencies.smk has CUDA drivers installed. (Automatically generated mags.yaml still disables GPU mode to avoid issues. User has to manually enable it before running the MAG generation step.)