chromo manual

Use chromo manual when you want to make reviewed assembly edits in a browser instead of asking ChromoSort to choose breakpoints or filters automatically. The command writes one HTML file with embedded CSS, JavaScript, reference/assembly metadata, contig ordering, and alignment rows. No external web assets are required.

The dashboard starts with every assembly contig present. Aligned contigs are ordered by reference FASTA order and reference coordinate. Unaligned contigs are kept at the end until you remove them.

chromo manual can combine sorting-style and fixing-style review in one human workflow: you can remove unaligned contigs, reorder pieces, invert pieces, add breakpoints, label scaffolds, and export a reviewed FASTA or recipe. Task modes chromo manual fix, chromo manual scaffold, and chromo manual gapfill add a focused review-event queue from chromo eval tables while keeping the same browse-around dashboard. The dot plots in the dashboard still come from the original coords or PAF file. After exporting a manual FASTA, re-run MUMmer or minimap2 before using that FASTA as the assembly input to chromo sort, chromo plot, chromo scaffold, or other alignment-dependent steps.

Run chromo manual

chromo manual \
  --ref-fasta reference.fa \
  --assembly-fasta assembly.fa \
  --coords mummer/sample.coords \
  --gfa assembly_graph.gfa \
  --output-html results/sample.manual.html \
  --suggested-output-fasta sample.manual.fa

The same dashboard can be generated from PAF:

chromo manual \
  --ref-fasta reference.fa \
  --assembly-fasta assembly.fa \
  --paf paf/sample.paf \
  --output-html results/sample.manual.html

Run A Task-Specific Manual Dashboard

chromo eval fix \
  --assembly-fasta assembly.fa \
  --coords mummer/sample.coords \
  --all \
  --output-prefix results/sample.eval_fix

chromo manual fix \
  --ref-fasta reference.fa \
  --assembly-fasta assembly.fa \
  --coords mummer/sample.coords \
  --review-table results/sample.eval_fix.fix_review.tsv \
  --gfa assembly_graph.gfa \
  --read-paf paf/reads_to_assembly.paf \
  --gaf graph_alignments/reads_to_graph.gaf \
  --output-html results/sample.manual_fix.html

The same pattern works for chromo manual scaffold with <prefix>.scaffold_review.tsv and chromo manual gapfill with <prefix>.gapfill_review.tsv. A task dashboard embeds the shared review events, shows them as a queue, and selecting an event focuses the corresponding contig or junction target when that source is present in the dashboard FASTA.

When --gfa is provided, the manual dashboard embeds per-contig graph context beside the dot plot review. Contig badges and details show whether the matching GFA node is present, whether its local neighborhood is simple, branching, or self-looped, node coverage tags such as RC:i, in/out degree, neighbor count, and oriented neighboring nodes. The selected-contig detail panel also shows immediate upstream/downstream graph neighbors, link orientation, overlap lengths, and whether each neighbor is aligned to the same best reference. This borrows the useful graph-inspection idea from Gap-Graph while keeping ChromoSort’s sequence-changing actions explicit in the manual recipe. An example graph-aware dashboard is shown in the output section below.

Task dashboards also expose modular evidence panels for the selected event. The alignment panel is always available because --coords or --paf is required. GFA, long-read PAF, and long-read GAF panels appear when the corresponding file is provided or when the review table contains matching graph_*, longread_*, or gaf_* fields from chromo eval. This keeps the dashboard useful when only one evidence stream exists, while making conflicting or complementary support visible when several streams were generated. The dashboard generator records optional --read-paf and --gaf paths and displays matching review-table fields; it does not independently recompute long-read support in the browser HTML.

For large genomes, the dashboard embeds alignment metadata but not full FASTA sequences by default. Open the HTML file in a browser, load the original assembly FASTA with the file picker, then export the edited FASTA. For tiny assemblies, demos, or tests, use --embed-sequences so the HTML can export FASTA without loading the source FASTA in the browser:

chromo manual \
  --ref-fasta reference.fa \
  --assembly-fasta assembly.fa \
  --coords mummer/sample.coords \
  --output-html results/sample.manual.html \
  --embed-sequences

Use the Manual Dashboard

The manual dashboard provides:

• A reference-ordered contig/piece list with every contig retained initially.
• A per-contig dot plot. Forward alignments are blue; reverse alignments are red. See the dot-plot guide for examples of common patterns to look for during review.
• Optional GFA node badges and neighbor details when generated with --gfa.
• An optional task-specific review-event queue when generated with --review-table.
• Modular evidence panels for alignment, GFA, long-read PAF, and long-read GAF support when those inputs or review-table fields are available.
• A graph filter for simple, branching, self_loop, and missing graph neighborhoods, plus a read-only neighborhood panel for the selected contig.
• A click-to-stage breakpoint position from the selected contig dot plot.
• Buttons to remove/restore a contig or piece, move it up/down, invert it, and add a breakpoint.
• A Remove unaligned button for quickly excluding unplaced contigs.
• A scaffold label for each active piece and a scaffold-export toggle that joins pieces with configurable N gaps.
• FASTA export and recipe JSON export.

Browser security prevents a static HTML file from silently overwriting arbitrary local paths. FASTA export is therefore a normal browser download, and the original FASTA is never modified.

Apply a Manual Recipe

The dashboard can export a recipe JSON file. Apply that recipe from the command line for reproducible runs:

chromo manual apply \
  --assembly-fasta assembly.fa \
  --recipe chromosort.manual.recipe.json \
  --output-fasta results/sample.manual.fa \
  --report results/sample.manual.tsv

Use --scaffold or --no-scaffold to override the recipe export mode, and --gap-bp to override the recipe gap size.

chromo manual Outputs

Example chromo manual Output

Table 1. Example chromo manual apply report rows. The command-line apply step writes the same piece-level audit information needed to reproduce a browser-reviewed recipe.

Listing 1. Example manual-apply FASTA records. Browser edits become ordinary FASTA records with the original source contig, slice interval, strand, and scaffold label in the header.

>contigA_manual001 original=contigA slice=1-80 strand=+ scaffold=chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>contigB_manual002 original=contigB slice=1-40 strand=+ scaffold=chr1
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

chromo manual Parameters