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Processed ABIF trace region

Export every processed ACGT trace sample in a selected ABIF region, with stored basecall anchors, all qualities, complete SVG pages and exact source bytes.

Browser-local processingInputOne processed ABIF101 / AB1 fileOutputTrace SVG pages, sample and basecall CSV, JSONUp to 16 MiB per file · File limit: 1
  1. 1Add input
  2. 2Adjust settings
  3. 3Get your result

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.ab1 · .abi · .abif

Up to 16 MiB per file · File limit: 1

    Options

    Complete the required options first. You can keep the defaults for the rest.

    Minimum 0 for samples, 1 for basecalls.

    Must be ≥ start and within the file; at most 8,000 selected samples.

    Preparing the tool…

    Before you start

    Export every processed ACGT trace sample in a selected ABIF region, with stored basecall anchors, all qualities, complete SVG pages and exact source bytes.

    How to use this tool

    1. Select one original AB1/ABIF file.
    2. Choose sample or basecall coordinates and enter inclusive start/end; basecall positions begin at 1.
    3. Export the region and check actual sample bounds, channel binding and whether quality is present.
    4. Keep every SVG page, complete sample/basecall CSV, report and original; copy or download the full report.

    Supported inputs and limits

    Choose exactly one original file, up to 16 MiB, with a filename up to 512 UTF-8 bytes. The content must match the finite processed ABIF101 profile; a .ab1 extension alone does not establish support. Input and filename stay in the browser.

    Uses processed DATA9–12 signed 16-bit channels and the FWO_1 ACGT permutation, with PBAS2 calls and strictly increasing PLOC2 anchors. Optional PCON2 retains unsigned qualities 0–255; absent quality is null, distinct from zero. Raw channels, smoothing and guessed calls are not supported.

    At most 5,000 directory entries, 500,000 points per channel and 40,000 basecalls. The four channels must have equal nonempty lengths. Calls may contain supported uppercase IUPAC DNA symbols; ambiguous calls remain labeled instead of being changed to ACGT.

    Choose sample indices from 0, inclusive at both ends, or basecall positions from 1, inclusive at both ends. For a base range, the first and last stored PLOC2 anchors become the sample bounds; no flank is added. Start/end must be safe integers, end ≥ start, and within this file.

    Select at most 8,000 samples. Each trace-NNN.svg page contains at most 500 selected samples and every A/C/G/T coordinate, with no thinning or smoothing. Negative stored values remain visible; all pages share the selected signed signal range including zero. A single-sample selection has four visible channel markers.

    Download report.json, samples.csv, basecalls.csv, every trace-NNN.svg page and original.input. samples.csv contains the complete selection; basecalls.csv and the report retain all source calls and qualities, including those outside the range. The original keeps every opaque tag byte.

    Complete files plus full report text are limited to 32 MiB. The report includes ordered directory metadata and payload hashes, channel binding, exact selection and all selected samples. Full report copy is byte-identical to report.json; a bounded preview does not shorten exports.

    A single 10-second deadline includes source checks, file reading, loading, processing, validation and first result display. Cancel or timeout publishes no late or partial result; the same original file and parameters can be retried. This is a finite processed profile, not full ABIF-standard certification or medical interpretation.

    Worked example

    Example input

    Synthetic processed ABIF101 file synthetic-trace.ab1 (1,378 bytes), with 128 points per channel and 16 calls. Below are all eight rows for samples 0–7; this is not an author attachment or experimental data.
    Example options
    {"rangeKind":"samples","start":0,"end":7}

    Example output

    sample_index,A,C,G,T
0,16,-12,-12,-12
1,34,-12,-12,-12
2,52,-12,-12,-12
3,70,-12,-12,-12
4,88,-12,-12,-12
5,70,-12,-12,-12
6,52,-12,-12,-12
7,34,-2,-12,-12

    When something does not work

    Keep the original. Correct the coordinate range or select at most 8,000 samples; base ranges must be checked against their stored anchors. Inspect malformed or unsupported payloads in an ABI-aware editor; renaming the extension does not repair them. Retry the same original File and options after cancel or timeout. Raw-channel files require another compatible reader.

    Frequently asked questions

    Why do samples and bases start differently?

    Samples are zero-based array indices; bases are one-based PBAS2 call positions. Both include end. A base range uses the first and last PLOC2 anchors and adds no flank.

    Is missing quality written as zero?

    No. An absent PCON2 produces null quality; a present zero remains numeric 0. An empty quality cell in CSV means missing; 0 means the stored value is zero.

    Are calls outside the region lost?

    No. The report and basecalls.csv retain every source call, anchor and quality. SVG labels only calls within the selection; samples.csv keeps A/C/G/T values for every selected sample.

    Does this process raw data or call bases again?

    No. This finite profile uses processed DATA9–12, FWO_1, PBAS2, PLOC2 and optional PCON2. It does not smooth, thin or call bases again, and does not claim the entire ABIF standard.

    Documentation & further reading

    Export a complete processed ABIF trace region →Keep trace samples and basecall coordinates together →

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