Command Reference

ChromoSort exposes one top-level command, chromo, with nine subcommands. Each subcommand page includes the purpose, examples, outputs, key parameters, and reasoning behind the command.

Command	Use it when you need to
`chromo sort`	assign contigs to reference sequences, filter duplicate overlaps, and write an ordered FASTA.
`chromo clean`	sort-filter raw contigs, conservatively fix retained contigs, and write a cleaned FASTA.
`chromo eval`	prepare editable TSV review tables for command-line or spreadsheet-first `fix`, `scaffold`, and `gapfill` curation, with optional graph and long-read evidence.
`chromo fix`	split reviewed or automatically detected chimeric contigs into reference-labeled pieces.
`chromo cut`	cut contigs at exact reviewed coordinates.
`chromo manual`	generate a browser dashboard for manual dot-plot review, task-specific review-event queues, modular evidence panels, and reproducible recipe export. See the dot-plot guide if the visual patterns are unfamiliar.
`chromo plot`	draw whole-genome, per-reference, or selected-reference dot plots from existing MUMmer coords or minimap2 PAF alignments. Use the dot-plot guide to interpret the patterns.
`chromo scaffold`	join final sorted contigs into one scaffold per reference sequence, with optional reviewed gap overrides and report-only graph junction evidence.
`chromo gapfill`	plan and optionally apply reviewed graph-supported fills between adjacent sorted contigs using guarded GFA paths and optional support evidence.