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Binit

🚧 Under Construction

This command is under active development and behavior or outputs may change.

Summary

Run integrated segment binning workflow

Description

Run an integrated segment-binning workflow over RdRp and CP contigs.

The workflow chains cluster, correlate, extend, and termini steps, then
joins their outputs to report candidate segment pairs with supporting
evidence from abundance/correlation and termini/motif consistency.

Usage

rolypoly binit [OPTIONS]

Options

  • --rdrp-fasta: Input FASTA containing RdRp candidate contigs (type: FILE; required; default: Sentinel.UNSET)
  • --cp-fasta: Input FASTA containing CP candidate contigs (type: FILE; required; default: Sentinel.UNSET)
  • -o, --outdir: Output directory for all intermediate and final workflow artifacts (type: DIRECTORY; required; default: Sentinel.UNSET)
  • -t, --threads: Threads used by cluster/extend/termini stages (type: INTEGER; default: 8)
  • --ani-min-identity: ANI identity threshold (0-1) used for cluster and extend (type: FLOAT RANGE; default: 0.9)
  • --ani-min-af: ANI aligned fraction threshold (0-1) used for cluster and extend (type: FLOAT RANGE; default: 0.8)
  • --min-correlation: Minimum correlation for the correlate stage (type: FLOAT; default: 0.01)
  • --min-prevalence: Minimum sample prevalence used in the correlate stage (type: FLOAT RANGE; default: 0.05)
  • --min-shared-samples: Minimum shared sample count used in the correlate stage (type: INTEGER RANGE; default: 1)
  • --termini-length: Termini length or range passed to rolypoly termini (type: TEXT; default: 4-1145)
  • --termini-distance: Maximum Hamming mismatch distance for termini seed grouping (type: INTEGER RANGE; default: 0)
  • --reuse-extend, --no-reuse-extend: Reuse existing extend outputs if present instead of rerunning extend (type: BOOLEAN; default: False)
  • --write-single-rdrp-strict, --no-write-single-rdrp-strict: Write strict candidate pairs that pass the complementarity check (type: BOOLEAN; default: False)
  • --log-file: Optional workflow-level log file path (type: FILE)