chromo plot

Use chromo plot when you already have a MUMmer coords or minimap2 PAF file and want a visual check without running mummerplot or re-aligning only for the plot. It writes PDF by default and can also write SVG or PNG. Forward-strand alignments are blue and reverse-strand alignments are red.

If you are learning how to read those patterns, start with How to Interpret Dot Plots. It explains axis orientation, forward and reverse segments, chimeric-looking contigs, inversions, duplicate or repeat-like signal, gaps, and common traps.

chromo plot never runs MUMmer or minimap2. It draws the alignment rows you give it. If those rows were generated from raw.fa, the plot still describes raw.fa, even when you also provide a chromo sort assignment report. The assignment report can reorder the query axis by kept sorted contigs, but it does not make a new alignment of <prefix>.ordered.fa.

After any FASTA-changing step, such as chromo sort outputting ordered.fa, chromo clean outputting clean.fa, chromo fix outputting fixed.fa, chromo cut, chromo manual export, or chromo scaffold, re-run MUMmer or minimap2 before using chromo plot to validate that changed FASTA.

Run chromo plot

Whole-genome plot from MUMmer coords:

chromo plot \
  --ref-fasta reference.fa \
  --assembly-fasta assembly.fa \
  --coords mummer/sample.coords \
  --output-prefix plots/sample

This writes plots/sample.pdf.

Whole-genome and per-reference plots from PAF, ordered by a chromo sort assignment report:

chromo plot \
  --ref-fasta reference.fa \
  --assembly-fasta assembly.fa \
  --paf paf/sample.paf \
  --assignments results/sample.contig_assignments.tsv \
  --output-prefix plots/sample \
  --per-ref \
  --sel-ref Gm6 Gm12 Gm15 \
  --formats pdf svg

When --assignments is provided, the query axis is ordered by the kept contigs in the assignment report. This is useful for reviewing a sorted ChromoSort order from the same alignment file that powered the sort. It is not equivalent to plotting the ordered.fa output; align ordered.fa separately if you want the plot to reflect the edited FASTA records.

Per-reference plots keep the x-axis on the full selected reference sequence, but compact each query row to the merged query coordinate spans covered by alignments to that selected reference. This keeps multi-reference contigs and large unaligned query gaps from adding unrelated vertical whitespace to each --per-ref panel. Axis tick units scale with the plotted length, using bp, kb, Mb, or Gb as appropriate for the current panel.

Use --sel-ref when you only want to replot one or a few reference sequences. For example, --sel-ref Gm6 Gm12 Gm15 limits the main plot to those reference sequences and, with --per-ref, writes only those per-reference panels.

chromo plot Outputs

Example chromo plot Output

Table 1. Example plot file set. A single run can write a whole-genome plot and, with --per-ref, one plot per reference sequence in each requested format.

chromo plot Parameters