Plot catalogue · Reads and molecules

Keep the evidence at molecule resolution

Use these tracks before reads have been collapsed into depth, a variant call or a site average. Each row or trace remains attributable to the molecule that produced it.

4 track types1 molecule per row

Contiguous alignmentPileupTrackReal CIGAR operations packed into rows, with strand, mapping quality and reference-aware mismatches.Open reference → Segmented alignmentSplitReadTrackOne row per molecule, one bar per segment and connectors that preserve visit order and orientation.Open reference → Modification patternBisulfiteTrackFilled and open calls per covered site, leaving truly uncovered positions empty rather than unmodified.Open reference → Raw currentSquiggleTrackNanopore signal as a min–max envelope at overview scale and the original trace when resolution allows.Open reference →

Choose by what was measured

Input still contains…	Start with
one reference position and CIGAR per read	PileupTrack
several alignments belonging to one molecule	SplitReadTrack
modified and unmodified calls along each molecule	BisulfiteTrack
current samples and a basecaller move table	SquiggleTrack

Related routes

• Signal and sequence after reads have become coverage or per-site fractions.
• Variation and association after molecule evidence has become a call.
• Recipes for piping SAM text from samtools and attaching a reference in Rust.