Exactly one target is compatible, so the read can be counted or written to the matching output.
Assignment reliability for known-target sequencing assays.
Know which read assignments you can trust.
DotMatch assigns fixed read windows to known short DNA targets and keeps the outcome visible for every read: unique, ambiguous, none, or invalid.
Use it when the guide, inline barcode, feature tag, primer or panel target, or whitelist sequence is already known and the important question is whether each read can be assigned safely.
More than one target is compatible, so DotMatch keeps the read out of forced calls.
No target is close enough, so the read remains available for unmatched-read review.
The requested read window cannot be extracted, so the failure is visible in QC.
Reliability failure modes
The risky reads are the point.
A known target list does not make every read safe to count. DotMatch is built around the cases that need to stay visible.
A read fits more than one target.
Ambiguity is reported as ambiguity instead of being hidden inside a count matrix.
The expected window is wrong.
Shifted barcode starts, short reads, and invalid extraction windows are surfaced before they become silent losses.
Correction would mix samples.
Target-library audits and barcode checks show when rescue settings can create unsafe assignments.
Unmatched reads carry signal.
Top-unmatched tables keep recurring off-target, adapter, or assay-design patterns available for review.
One workflow across assay contexts
The reliability layer is the same.
CRISPR guides, inline barcodes, feature tags, primers, panel targets, and whitelist sequences all reduce to the same auditable assignment question.
CRISPR guidesinline barcodesfeature tagsprimers / panelswhitelists
Declare the known targets.
Use the guide, inline barcode, feature tag, primer or panel target, or whitelist sequences you expect for the assay.
Assign the same read window.
DotMatch extracts the configured window from each read and evaluates it against the target list under the recorded run settings.
Review outcomes with artifacts.
Counts, split FASTQs, QC tables, unmatched reads, ambiguity rows, summaries, and reports stay connected to the assignment decision.
Auditable evidence
Claims stay tied to checks.
Speed is useful only after the assignment rule is clear. DotMatch keeps performance, correctness, and packaging statements scoped to repository evidence, public artifacts, and install smoke tests.
What the homepage can safely claim
DotMatch is a deterministic known-target assignment system for short read windows. It records explicit read outcomes and writes ordinary workflow artifacts that can be inspected outside the homepage.
Broader claims about alignment, basecalling, downstream screen analysis, production demultiplexing replacement, calibrated probabilities, or unbounded assay coverage remain outside the public claim boundary unless the linked evidence says otherwise.
Local installation
Run assignment reliability checks locally.
DotMatch is a local command-line and Python package. Keep sequencing data on your machine, install the package, and cite the software release through the repository citation metadata.
pip install dotmatch
dotmatch --help