Parameters: setDadaOpt() parity

dada2-rs aims to mirror R DADA2's algorithm parameters faithfully. Every result-affecting option from R's setDadaOpt() (the dada_opts defaults in dada.R) is exposed as a CLI flag with the same default value, so a stock dada2-rs run reproduces a stock R run.

Equivalency table

R dada_opts	R default	dada2-rs flag	dada2-rs default	match
OMEGA_A	1e-40	--omega-a	1e-40	✅
OMEGA_P	1e-4	--omega-p	1e-4	✅
OMEGA_C	1e-40	--omega-c	1e-40 (dada) / 0 (learn)	✅ †
DETECT_SINGLETONS	FALSE	--detect-singletons	false	✅
USE_KMERS	TRUE	--no-kmer-screen	on	✅
KDIST_CUTOFF	0.42	--kdist-cutoff	0.42	✅
MAX_CONSIST	10	--max-consist (learn)	10	✅
MATCH	5	--match	5	✅
MISMATCH	-4	--mismatch	-4	✅
GAP_PENALTY	-8	--gap-p	-8	✅
BAND_SIZE	16	--band	16	✅
MAX_CLUST	0	--max-clust	0	✅
MIN_FOLD	1	--min-fold	1	✅
MIN_HAMMING	1	--min-hamming	1	✅
MIN_ABUNDANCE	1	--min-abund	1	✅
USE_QUALS	TRUE	--use-quals	true	✅
HOMOPOLYMER_GAP_PENALTY	NULL	--homo-gap-p	→ --gap-p	✅ ‡
GREEDY	TRUE	--greedy	true	✅
PSEUDO_PREVALENCE	2	--pseudo-prevalence	2	✅
PSEUDO_ABUNDANCE	Inf	--pseudo-min-abundance	off (= Inf)	✅
VECTORIZED_ALIGNMENT	TRUE	— (always on)	—	◻︎ perf
GAPLESS	TRUE	— (always on)	—	◻︎ perf
SSE	2	— (Rust autovectorizes)	—	◻︎ N/A

These flags apply to the denoising and error-learning subcommands (dada, dada-pooled, dada-pseudo, learn-errors, errors-from-sample). remove-bimera-denovo additionally honors --match / --mismatch / --gap-p, matching R's removeBimeraDenovo (which respects the global GAP_PENALTY).

Notes

• † OMEGA_C — the base dada_opts default is 1e-40, but learnErrors() overrides it to 0 internally (error inference shouldn't merge by abundance p-value). dada2-rs encodes the same split: 1e-40 for the dada* commands, 0 for learn-errors. It is not inherited via --inherit-err-params.

• ‡ HOMOPOLYMER_GAP_PENALTY = NULL — in R, NULL means "score homopolymer gaps with the normal GAP_PENALTY." dada2-rs reproduces this: when --homo-gap-p is unset it falls back to whatever --gap-p resolves to (so --gap-p -4 alone yields homo_gap_p = -4), rather than pinning a literal default.

• Scalar MATCH / MISMATCH — R's full 4×4 SCORE_MATRIX is commented out in dada.R; the active path uses the scalar MATCH/MISMATCH (uniform +5 diagonal / −4 off-diagonal). dada2-rs matches that active path.

• VECTORIZED_ALIGNMENT / GAPLESS / SSE — deliberately not exposed. These are implementation/performance toggles, not algorithm parameters: dada2-rs always uses its vectorized banded aligner, and SSE = 2 (R's SSE2 selection) is moot since the Rust kernel autovectorizes (with AVX2/AVX-512 available via a release-native build). They are result-equivalent.

Beyond setDadaOpt(): --kmer-size

KMER_SIZE is not a setDadaOpt() option — R fixes the k-mer screen at k = 5 in its C layer. dada2-rs exposes it as a tunable flag, --kmer-size (3–8, default 5). The default matches R exactly, but the knob lets PacBio HiFi runs trade memory for speed (e.g. k = 7); see the PacBio walkthrough. This is the one place dada2-rs goes beyond R's parameter surface.