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Changelog

All notable changes to this project are documented here. The format is based on Keep a Changelog, and the project aims to follow Semantic Versioning (pre-1.0, so minor versions may carry breaking changes).

0.2.0 - Unreleased

Added

  • summary subcommand: per-position quality metrics, cumulative expected-error metrics, and an optional per-read sequence-complexity histogram (#8).
  • sample and errors-from-sample subcommands for subsampling input FASTQs and learning an error model from the subsample (usable for bootstrapping).
  • --failed-uniques diagnostic on dada / dada-pseudo / dada-pooled: emits a TSV of uniques that failed to seed a partition (#60).
  • chimera-diagnostics for higher-order (trimera) screening, with nearest-parent and flank gates (#54).
  • Experimental WFA alignment backend (--align-backend wfa2) with a --wfa-max-edits edit-budget cap (#49, #51). ASV-equivalent to Needleman- Wunsch on tested Illumina and PacBio HiFi data, but not byte-identical.
  • dada-pooled --gzip writes the per-sample JSON files gzip-compressed as {sample}.json.gz (#70). dada and dada-pseudo gain the same --gzip flag, for consistency across the per-sample denoisers.
  • merge-pairs records input-file provenance and warns on mismatch (#10).
  • just / make task runners for build, install, test, and docs (#46).

Fixed

  • learn-errors and errors-from-sample now gzip-compress their output when the -o path ends in .gz, for consistency with the other JSON-emitting subcommands (previously the file was written uncompressed) (#71).
  • kdist-calibrate --from-dada now resolves derep inputs whose filenames were renamed by the pipeline (e.g. {sample}.derep.R1.json.gz): it falls back from the exact {sample}.json[.gz] match to a {sample}.*.json[.gz] scan, disambiguating an ambiguous prefix by the derep JSON's own sample field (#72).
  • kdist-calibrate --from-dada now reads gzip-compressed dada output JSONs (*.json.gz, e.g. from dada-pooled --gzip); previously the gzip bytes were parsed as raw JSON and failed with expected value, line 1 column 1.
  • make-sequence-table now reads gzip-compressed dada / merge-pairs inputs (*.json.gz, e.g. from dada --gzip / dada-pooled --gzip); previously the gzip bytes were parsed as raw JSON and failed with expected value, line 1 column 1.
  • Single-file JSON -o outputs now honor a .gz output path, routing through the shared gzip-aware writer instead of a raw write (matching learn-errors, #71): summary, summary-merge, merge-pairs, remove-primers, filter-and-trim, make-sequence-table, remove-bimera-denovo, assign-taxonomy, assign-species, and dada's single-sample output.

Changed

  • The experimental WFA backend is now gated behind an off-by-default wfa Cargo feature (#63). Default builds — and the published crate — are Needleman-Wunsch only; selecting --align-backend wfa2 without the feature errors rather than silently falling back to NW. Building WFA requires a source checkout (cargo build --features wfa) because it depends on a git crate that cannot ship on crates.io.
  • Denoising/error-learning verbose logs now echo the active alignment backend (#51).
  • Trimmed the published crate: development, benchmarking, concordance data (multi-MB PacBio FASTQs), examples, notes, and CI/infra files are excluded.

Performance

  • Sparse k-mer-8 screen, gated to k ≥ 8, cutting resident memory in the high-k regime (#43).
  • dada-pooled streams dereplication into merging instead of holding all dereps in memory, and uses an integer merge-quality accumulator (#39, #41).
  • Various k-mer-vector memory reductions in the alignment screen (#32).

CI

  • R DADA2 concordance guardrail for Illumina and PacBio, with abundance/recall/ precision gates (#35).

0.1.0 - 2026-06-03

  • Initial crates.io release: Rust ports of the core DADA2 pipeline steps (filter-and-trim, derep, learn-errors, dada, merge-pairs, remove-bimera-denovo, assign-taxonomy / assign-species, sequence-table helpers).