consensus_from_traces
Read-only
Merge one or two Sanger reads into a consensus with the ported SeqTrace caller. With two reads (typically a forward and a reverse of the same amplicon) an IUPAC ambiguity code marks a position the two DISAGREE about; with one read there is nothing to disagree with and a code marks a position where no single base cleared the confidence bar. Returns the consensus, how many positions are ambiguous, and how many the consensus's own trimming stage cut from the ends.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| document | No | the first read: its name or its project file id. | |
| min_conf | No | the confidence a base must clear to be called rather than written as a code. SeqTrace range 1-61. | |
| algorithm | No | Bayesian converts each base's Phred to a posterior and combines the reads position by position; legacy lets the higher-confidence base win each position outright. They are different callers, not settings of one. | Bayesian |
| trim_window | No | how many consensus bases the quality-trim mean is taken over. Wider is more forgiving of a single bad base and slower to stop at a genuinely bad end. Advanced. | |
| primer_match | No | the fraction of a primer that must match for it to be cut. 1 is exact; lower tolerates the mismatches a real read carries at its noisy start. Only applies when trim_primers is true. Advanced. | |
| quality_trim | No | trim the consensus's own ends by quality. Note this is the stage primer trimming lives inside, so primer trimming does nothing without it. | |
| trim_primers | No | cut the primers off the consensus ends. It runs INSIDE the quality-trim stage, so turning it on turns that stage on too. | |
| trim_end_gaps | No | also cut the gap runs at each end, where only one read reached. With two reads those stretches are single-read consensus and read as agreement when they are not. Advanced. | |
| trim_min_good | No | how many of those bases must clear `min_conf` for the window to be kept. It cannot exceed `trim_window` and is clamped to it rather than refused. Advanced. | |
| forward_primer | No | the forward primer to cut, 5→3. Only applies when trim_primers is true. | |
| reverse_primer | No | the reverse primer to cut, 5→3. Only applies when trim_primers is true. | |
| second_document | No | the second read, usually the reverse of the same amplicon. Leave empty for a single-read consensus, which is a different question and is reported as one. | |
| reverse_complement_second | No | reverse-complement the second read before merging. A reverse read of the same amplicon needs this; two forward reads do not. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| length | Yes | its length in bases | |
| reading | Yes | the same sentence the editor shows for this run, generated from it | |
| consensus | Yes | the consensus, compact (no spacers) — what you would export or align | |
| readsUsed | Yes | how many reads went in. With 1, an ambiguity is low confidence; with 2, it is disagreement | |
| trimmedFromEnds | Yes | positions the consensus's own trimming stage removed | |
| ambiguousPositions | Yes | positions written as an IUPAC code. Wire it into a gate — but read `readsUsed` first, because the number means two different things |