screen_contamination
Read-only
Screen a nucleotide sequence for vector, adapter, linker and primer contamination against NCBI's UniVec, using VecScreen's own BLASTn parameters and category rules. Reports every match graded Strong/Moderate/Weak plus the short 'suspect origin' stretches NCBI asks to be removed with the vector, and emits both the N-masked sequence and the longest clean region so a pipeline can gate on the result or carry the clean part onward.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| dust | No | mask low-complexity sequence for SEEDING only (`-dust yes -soft_masking true`): a seed may not START in masked sequence, but an extension may run through it, so a genuine match spanning a repeat is not truncated. Advanced. | |
| build | No | which UniVec build to search: 'core' is NCBI's curated 3,155-segment subset and is what routine screening should use; 'full' is the complete 6,111-segment set — more sensitive, and more redundant hits. | core |
| _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. | |
| reward | No | score for a matching base (`-reward`). Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. | |
| penalty | No | score for a mismatching base, NEGATIVE (`-penalty`). With reward 1 and penalty −5 only a near-exact stretch can score above the reporting floor, which is what makes VecScreen specific. Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. 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. | |
| gap_open | No | cost to open a gap (`-gapopen`); a gap of length k costs `gapopen + k * gapextend`. Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. | |
| sequence | No | the nucleotide sequence to screen; leave empty to screen the open record. A protein sequence is refused — this is a nucleotide search. | |
| min_score | No | lowest raw score worth reporting — VecScreen's weakest reportable match. Lowering it reports more and specifies less. Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. | |
| word_size | No | exact-match seed length (`-word_size`). A sequence shorter than this cannot be screened at all, and the engine says so. Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. | |
| gap_extend | No | cost per gapped base (`-gapextend`). Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. | |
| internal_weak | No | raw score at or above which an internal match is reported at all, as Weak. NCBI leaves a deliberate gap here: an internal match scoring 16-22 is not reportable, because an internal match needs more evidence than a terminal one. Each ladder must stay in order (strong >= moderate >= weak) or the lower rungs become unreachable, and the run is refused rather than graded. Advanced. | |
| terminal_weak | No | raw score at or above which a terminal match is reported at all, as Weak. Below this a terminal match is not reported. Each ladder must stay in order (strong >= moderate >= weak) or the lower rungs become unreachable, and the run is refused rather than graded. Advanced. | |
| x_drop_gapped | No | X-drop for the preliminary gapped pass, in score units (`-xdrop_gap`, converted); capped at each seed’s own ungapped score. Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. | |
| internal_strong | No | raw score at or above which an internal match — one that is not terminal — is graded Strong. Each ladder must stay in order (strong >= moderate >= weak) or the lower rungs become unreachable, and the run is refused rather than graded. Advanced. | |
| terminal_strong | No | raw score at or above which a terminal match is graded Strong. A terminal match — one reaching within `terminal_distance` of an end of the query or of another reported region — is believed on less evidence than an internal one, which is why the two ladders differ. Each ladder must stay in order (strong >= moderate >= weak) or the lower rungs become unreachable, and the run is refused rather than graded. Advanced. | |
| ungapped_cutoff | No | lowest ungapped score that sends a seed to gapped extension — blastn’s gap trigger, converted from 27 bits. Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. | |
| x_drop_ungapped | No | X-drop for ungapped extension, in score units. It bounds extension; it does not change which alignment is optimal. Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. | |
| internal_moderate | No | raw score at or above which an internal match is graded Moderate. Each ladder must stay in order (strong >= moderate >= weak) or the lower rungs become unreachable, and the run is refused rather than graded. Advanced. | |
| terminal_distance | No | how close to an end of the query — or to another reported region — a match must reach to count as terminal and be graded on the lower of the two ladders. NCBI's published value is 25 bases. Advanced. | |
| terminal_moderate | No | raw score at or above which a terminal match is graded Moderate. Each ladder must stay in order (strong >= moderate >= weak) or the lower rungs become unreachable, and the run is refused rather than graded. Advanced. | |
| suspect_origin_max | No | length under which a stretch of non-vector sequence stranded between two matches (or between a match and an end) is reported as 'suspect origin' — too short to have come from anywhere trustworthy, so NCBI asks for it to be removed with the vector. Advanced. | |
| x_drop_gapped_final | No | X-drop for the traceback that produces the reported alignment, in score units (`-xdrop_gap_final`, converted). Default is NCBI's published VecScreen setting; changing it means the result is no longer VecScreen's. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| worst | Yes | the highest category present — strong | moderate | weak | suspect — or 'clean' when nothing was found. The slot to branch a pipeline on | |
| matches | Yes | every raw match, one per database record: coordinates, strand, score and the UniVec entry hit | |
| segments | Yes | the merged contaminated regions, each with its coordinates and category — what the map draws | |
| cleanSequence | Yes | the longest stretch carrying no match at all — wire it onward when the screen is a trimming step rather than a gate. Empty when nothing clean is left | |
| maskedSequence | Yes | the query with every match and suspect-origin stretch replaced by N — the form NCBI asks a submitter to upload | |
| contaminatedPct | Yes | percentage of the query covered by at least one reported match — the slot to gate on numerically |