MetaPilot v1.0.0-beta.6 (Beta)

Release notes – MAG workflow options
Major update: more control over MAG genome selection
This release adds configurable options in the MAG (Metagenome-Assembled Genomes) workflow so you can match the pipeline to your study goals (speed vs depth, marker set, etc.).

1. Genome selection: Marker 2 vs Marker 4
   🧩Marker 2 (rib_elon)
   Uses ribosomal and elongation-factor markers only.
   Greedy selection with knee-based stopping.
   Best when you want a fast, simple workflow or when 4-markers are not available.
   🧩Marker 4 (Marker4_highpep)
   Uses four marker categories (Ribosomal, Replication, Elongation, Synthetase).
   Requires Marker4_highpep.fasta and genomes-taxa.tsv (can be generated from the UI).
   Supports privilege species and auto-representative selection, then knee-based stopping.
   Best when you want higher-confidence, taxonomy-aware genome selection.
   You choose the mode in the Parameters tab for both pFind and Sage MAG workflows.
2. Selection strategy: Focus vs Comprehensive
   🧩Focus
   Stops at an earlier knee (median of Kneedle, Curvature, Slope).
   Fewer genomes, faster runs and reports.
   Suited to exploratory or high-confidence analyses.
   🧩Comprehensive
   Stops at a later knee (max of Chord-distance, Piecewise).
   More genomes, deeper coverage.
   Suited to maximising detected diversity or downstream diversity/taxonomy analyses.
   This is the “Selection strategy” in the same Parameters section.

Summary
Marker 2 / Marker 4: choose marker set and input requirements (no files vs 4-markers + taxonomy).
Focus / Comprehensive: choose how many genomes to keep after knee-based stopping.
Together, these options let you tune the MAG workflow for your specific research goal (speed, simplicity, confidence, or coverage) from the same UI in both pFind and Sage MAG workflows.

If the pFind workflow doesn't work well, please try to download the latest version of pFind (https://github.com/pFindStudio/pFind3) then set the path in the Resource configuration.

🧩 About Resources Pack
MetaPilot requires a large Resources Pack available from the previous release (v1.0.0-beta.1).
➡️ Download it here:
👉 MetaPilot Resources Pack (from v1.0.0-beta.1)
You only need to download this pack once — all future versions of MetaPilot will use the same resource files.