Chromatogram

1. 01Four-channel trace viewer with adjustable zoom and peak-height scale
2. 02Per-base Phred quality track, with mean quality and the percentage of bases at or above Q20 and Q30
3. 03Base call editing by click or arrow key, with undo and redo held separately from the trace data
4. 04Numeric start and end trim bounds
5. 05Reverse complement, which re-reads the trace in the flipped orientation
6. 06Secondary (mixed) peak detection reported as IUPAC ambiguity codes
7. 07Consensus building across grouped traces, by the legacy and the Bayesian method
8. 08Fitting (glocal) alignment of the read to a reference, with automatic orientation and origin-spanning placement on circular sequences
9. 09Variant table of substitutions, insertions and deletions, each row clickable to its position
10. 10Variant consequence classification (silent, missense, nonsense, indel) read in the covering CDS frame and strand, under a selectable NCBI genetic code
11. 11Peak inspection per base: per-channel amplitudes, position, confidence, and the second-peak ratio

The trace engine is a TypeScript port of SeqTrace, cfutils and sangerseqR, validated byte for byte against those libraries with golden vectors. The panel runs on @ports/basecall, @ports/chromatogram, @ports/msa, @ports/verify.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Can I open an .ab1 file without installing software?

Yes. The parser runs in the browser, so an .ab1, .abi, .scf or .ztr file opens by loading it into the page. Nothing is uploaded to a server.

Can I edit base calls and keep the trace intact?

Yes. Edited bases are stored separately from the parsed trace, and undo and redo apply to the edits only, so the original chromatogram data is never overwritten.

Does it call variants against a reference?

Yes. The read is aligned to the reference with a fitting (glocal) alignment, and mismatches are listed as substitutions, insertions or deletions. When the reference carries CDS features, each substitution is classified in that CDS frame and strand.