ligate_fragments
Ligate fragments by their overhangs (pydna ligation_assembly) — sticky, optionally blunt. Each input may be digested by its own enzymes first, which is the digest → ligate hand-off. Emits the first product as a NEW record.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| blunt | No | allow blunt-end joins as well as sticky. | |
| _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. | |
| enzymes | No | digest every input with these enzymes before ligating. Left unset, the run uses your active enzyme collection. | |
| fill_in | No | positional booleans: fill that input's 5' overhangs with Klenow after its digest, so its cut ends join blunt (needs `blunt`). Each join then reports the bases the fill-in added. Advanced. | |
| _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. | |
| fragments | No | the fragments to ligate — wire upstream `record` outputs here, or name library documents. | |
| end_origins | No | what MADE each input's ends, positionally — this fixes the 5'-phosphate before any treatment. Leave empty for `unspecified`, which is treated as phosphorylated and reproduces a run with no end chemistry at all. Advanced. | |
| circular_only | No | report only circular products. | |
| end_treatments | No | the phosphatase or kinase applied to each input AFTER it was made, positionally. Dephosphorylating the vector is what stops it self-ligating; a junction with no 5'-phosphate on either strand forms no bond and the product is dropped. Advanced. | |
| include_subject | No | also include the node's subject as a fragment. | |
| fragment_indices | No | which band to take from each input's digest, positionally (0 = first fragment). Leave empty to use every fragment — which frequently yields no product, exactly as at the bench. | |
| allow_partial_overlap | No | allow partially overlapping sticky ends. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| layout | Yes | where each piece and join sits ON the product: the spans the map draws | |
| record | Yes | the first ligation product, as a record | |
| products | Yes | every product | |
| junctions | Yes | the junctions formed, with the overhang each was made by | |
| productCount | Yes | number of products (>1 = ambiguous ligation) | |
| nickedJunctions | Yes | indices of junctions left NICKED by a missing 5'-phosphate on one strand — the product still transforms and is repaired in vivo. Empty when every junction sealed |