ChromoSort Documentation

ChromoSort is a reference-guided assembly curation toolkit for sorting contigs, conservatively cleaning mostly-correct assemblies, splitting reviewed chimeric contigs, making manual cuts, reviewing dot plots, scaffolding ordered contigs, applying reviewed graph-supported gap fills, and plotting existing whole-genome alignments.

This documentation is organized as a user guide for installing ChromoSort, preparing inputs, running common workflows, and reading command outputs.

The most important workflow rule is that alignment evidence matches one exact FASTA pair. MUMmer coords or minimap2 PAF generated from raw.fa can support multiple decisions about raw.fa, but edited outputs such as ordered.fa, fixed.fa, manual FASTA exports, and scaffold FASTAs need fresh alignments before they are used as inputs to another alignment-dependent command.

Start Here

• Installation
• Input files
• Workflows
• Agent and review playbook
• Agent readiness roadmap
• Agent task recipes
• Concepts for dot plots, contig fixing, scaffolding, and gap filling.
• Guides for ChromoSort-specific evidence, command, review, and worked-example guides.
• Command reference
• Production upgrade roadmap

Commands

• chromo sort
• chromo clean
• chromo eval
• chromo fix
• chromo cut
• chromo manual
• chromo gafprep
• chromo plot and dot-plot interpretation
• chromo graph-map
• chromo scaffold
• chromo gapfill

Running Analyses

• Output files
• Concepts for the educational framework behind plotting, fixing, scaffolding, and gap filling.
• Guides for ChromoSort command decisions, reports, reviewed plans, sequence-changing outputs, worked review paths, and handoff checklists.
• Agent and review playbook for choosing one primary coords or PAF alignment, inversion review, long-read/GFA/GAF evidence, and handoffs between chats or projects.
• Agent readiness roadmap for coding-agent setup, shared checks, and implementation guardrails.
• Agent task recipes for change-type checklists that map files, docs, and tests.
• Architecture for algorithm, data-model, evidence, and command-activation details.
• Production upgrade roadmap
• Troubleshooting

Project Information

• Current status and version history
• Contributing

Main Workflow

1. Generate MUMmer show-coords or minimap2 PAF alignments between the reference and assembly.
2. For mostly-correct assemblies, use chromo clean for conservative sort-filter-fix cleanup, then re-align the cleaned FASTA.
3. For more complex cases, use chromo plot and the dot-plot guide, then use chromo manual when helpful to inspect suspicious contigs.
4. Use chromo eval and task-specific chromo manual dashboards when outlier fix, scaffold, or gapfill decisions need table or GUI review.
5. Use chromo eval all plus chromo gafprep when targeted GAF evidence is needed across fix, scaffold, and gapfill review without a full-depth read-to-graph alignment.
6. Use chromo fix or chromo cut for reviewed sequence edits.
7. Re-align the fixed assembly.
8. Use chromo sort to assign, filter, orient, and order contigs.
9. Re-align again if a later command should operate on ordered.fa rather than on the original assembly and its assignment report.
10. Use chromo graph-map or chromo plot --gfa-overlay when unitig-level GFA features need to be projected onto contig FASTA coordinates.
11. Use chromo scaffold to build one scaffold per reference sequence.
12. Use chromo gapfill only when reviewed GFA paths should replace N gaps.