Oligo/adapter prefix assignment: TruSeq R1 public lane

• Category: Public data

• Assay type: oligo_adapter

• Evidence level: Documented example

• Dataset: fast-adapter-trimming TruSeq R1 fixed-window sample

• Condition shown: Fixed-window adapter-prefix assignment with exact-slice baseline agreement.

• Primary report: docs/benchmarks/oligo_adapter/README.md

What This Shows

• DotMatch can assign known oligo/adapter prefixes in a fixed read window.

• The report distinguishes assignment from trimming.

What It Does Not Show

• This is not adapter trimming evidence.

• Primer removal, UMI grouping, and read merging are outside this lane.

Comparator And Validation

Comparator semantics: The public lane uses a fixed R1 window and deduplicated TruSeq adapter-prefix targets, with a transparent exact-slice baseline for fixed-window assignment.

Validation: The public gate requires DotMatch k=0 and k=1 rows, an exact-slice baseline, zero validation mismatches, k=0 agreement with the baseline, and k=1 assignment count no lower than k=0.

Report Examples

• Oligo/adapter benchmark report (markdown)

Raw Artifacts

• benchmarks/raw/oligo_adapter.csv

• examples/oligo_adapter/data/metadata.json

Reproduce Or Check

• make bench-oligo-adapter-public

• make oligo-adapter-public-gate