Oligo/Adapter Assignment Evidence

This report covers fixed-window assignment of short adapter-like oligos with DotMatch’s known-target counting layer.

The synthetic lane checks exact, one-substitution, ambiguous, and unmatched adapter-like oligos. The public lane uses the fast-adapter-trimming TruSeq R1 fixture and validates DotMatch k=0 against a transparent exact-slice hash baseline over the documented fixed window.

Synthetic Command

dotmatch count --targets benchmarks/work/oligo_adapter/adapter_oligos.tsv --reads benchmarks/work/oligo_adapter/adapter_reads.fastq --sample-label oligo_adapter_fixture --target-start 0 --target-length 12 --k 1 --metric hamming --format dotmatch --out benchmarks/work/oligo_adapter/adapter_counts.tsv --summary benchmarks/work/oligo_adapter/adapter_summary.json --assignments benchmarks/work/oligo_adapter/adapter_assignments.tsv --ambiguous report --sample-qc benchmarks/work/oligo_adapter/adapter_sample_qc.tsv

Raw Rows

tool	workflow	status	targets	reads	start	length	k	metric	assigned	exact	corrected	ambiguous	unmatched
dotmatch_count	synthetic_oligo_adapter_fixture	smoke	3	6	0	12	1	hamming	2	1	1	3	1
dotmatch_count	public_fast_adapter_truseq_r1	supported	9	10000	229	20	0	hamming	156	156	0	0	9844
dotmatch_count	public_fast_adapter_truseq_r1	supported	9	10000	229	20	1	hamming	159	156	3	0	9841
exact_slice_hash	public_fast_adapter_truseq_r1	supported	9	10000	229	20	0	exact	156	156	0	0	9844

Public Adapter-Prefix Lane

Dataset: fast-adapter-trimming 788707_20180313_S_R1.small.fastq.gz with adapters/truseq.fa target prefixes.
Source repository: https://github.com/linsalrob/fast-adapter-trimming
Source license: MIT, as reported by the upstream GitHub repository metadata.
Fixed window: DotMatch uses --target-start 229 --target-length 20 on R1.
Comparator semantics: the exact-slice hash baseline counts reads whose fixed R1 substring exactly matches a deduplicated TruSeq adapter-prefix target. It validates fixed-window assignment semantics, not trimming correctness.

Public Commands

dotmatch count --targets examples/oligo_adapter/data/adapter_oligos.tsv --reads examples/oligo_adapter/data/788707_20180313_S_R1.small.subsample10000.fastq.gz --sample-label fast_adapter_truseq_r1 --target-start 229 --target-length 20 --k 0 --metric hamming --format dotmatch --out benchmarks/work/oligo_adapter/public_fast_adapter_truseq_r1_k0_counts.tsv --summary benchmarks/work/oligo_adapter/public_fast_adapter_truseq_r1_k0_summary.json --assignments benchmarks/work/oligo_adapter/public_fast_adapter_truseq_r1_k0_assignments.tsv --ambiguous report --sample-qc benchmarks/work/oligo_adapter/public_fast_adapter_truseq_r1_k0_sample_qc.tsv

dotmatch count --targets examples/oligo_adapter/data/adapter_oligos.tsv --reads examples/oligo_adapter/data/788707_20180313_S_R1.small.subsample10000.fastq.gz --sample-label fast_adapter_truseq_r1 --target-start 229 --target-length 20 --k 1 --metric hamming --format dotmatch --out benchmarks/work/oligo_adapter/public_fast_adapter_truseq_r1_k1_counts.tsv --summary benchmarks/work/oligo_adapter/public_fast_adapter_truseq_r1_k1_summary.json --assignments benchmarks/work/oligo_adapter/public_fast_adapter_truseq_r1_k1_assignments.tsv --ambiguous report --sample-qc benchmarks/work/oligo_adapter/public_fast_adapter_truseq_r1_k1_sample_qc.tsv

python3 scripts/bench_oligo_adapter.py --include-public --metadata examples/oligo_adapter/data/metadata.json

Scope

These lanes verify fixed-window known-oligo/adapter assignment, one-substitution rescue, and explicit ambiguous/unmatched diagnostics. Run make oligo-adapter-smoke-gate for smoke evidence and make oligo-adapter-public-gate for the public lane. The public lane checks adapter-prefix assignment for the recorded R1 window. Primer removal, UMI grouping, read merging, and adapter-trimming workflows need separate comparator records.