Issues

• perf: vectorize the homopolymer gap penalty (--homo-gap-p) in the aligner

  enhancementlow priority
  HPCBio/dada2-rs#304 · Filter by author cjfields opened on Oct 23, 2026

• [pre-cite] GPU-accelerated DADA2 in Rust already exists — ecoPrimals wetSpring

  HPCBio/dada2-rs#303 · Filter by author ecoPrimal opened on Oct 23, 2026

• Carry denoising provenance (params, error-model identity) into dada output and the sequence table

  enhancement
  HPCBio/dada2-rs#297 · Filter by author cjfields opened on Oct 20, 2026

• perf: exact presence-bitmap bound in front of kmer_dist8 for screen-dominated pools

  experimentlow priority
  HPCBio/dada2-rs#295 · Filter by author cjfields opened on Oct 20, 2026

• Experiment: indel-aware splitting and λ (after the next crates.io release)

  enhancementexperiment
  HPCBio/dada2-rs#291 · Filter by author cjfields opened on Oct 19, 2026
  3

• Does a tighter k-mer screen let WFA beat NW? (--kdist-cutoff × backend)

  enhancementexperiment
  HPCBio/dada2-rs#290 · Filter by author cjfields opened on Oct 19, 2026
  1

• Opt-in alignment end model for primer-anchored amplicons (global / end-free-only)

  enhancementexperiment
  HPCBio/dada2-rs#289 · Filter by author cjfields opened on Oct 18, 2026
  4

• merge-pairs: R's prefer consensus at --max-mismatch > 0 (needs n0 in dada output)

  enhancementlow priority
  HPCBio/dada2-rs#274 · Filter by author cjfields opened on Oct 6, 2026
  1

• OMEGA_A on indel-rich amplicons (ITS2): measure near-misses against the member-order floor

  enhancementlow priority
  HPCBio/dada2-rs#246 · Filter by author cjfields opened on Sep 30, 2026
  7

• learn-errors: record the training samples in the error model (and optionally write the training derep)

  enhancement
  HPCBio/dada2-rs#245 · Filter by author cjfields opened on Sep 29, 2026
  1

• Decide which --verbose lines to drop now that --metrics-json carries them

  HPCBio/dada2-rs#236 · Filter by author cjfields opened on Sep 28, 2026

• Feature: primer summary details

  enhancement
  Feature

  HPCBio/dada2-rs#230 · Filter by author cjfields opened on Sep 27, 2026

• OMEGA_C was parked alongside OMEGA_A and is still unanswered — and it needs a different instrument

  low priority
  HPCBio/dada2-rs#228 · Filter by author cjfields opened on Sep 27, 2026

• Benchmark assign-taxonomy head-to-head vs R (the reference-size axis is untested)

  HPCBio/dada2-rs#186 · Filter by author cjfields opened on Sep 22, 2026
  1

• More concise code comments where possible

  HPCBio/dada2-rs#179 · Filter by author cjfields opened on Sep 21, 2026
  2

• Docs build: prepare for the MkDocs 2.0 / Material breaking changes

  HPCBio/dada2-rs#170 · Filter by author cjfields opened on Sep 19, 2026
  3

• Umbrella: mock-community truth sets (incl. an Illumina set on the same mock)

  HPCBio/dada2-rs#166 · Filter by author cjfields opened on Sep 14, 2026
  2

• Conciseness review

  HPCBio/dada2-rs#164 · Filter by author cjfields opened on Sep 14, 2026

• Benchmark checklist: does R DADA2 gain as much from NUMA binding as dada2-rs?

  HPCBio/dada2-rs#155 · Filter by author cjfields opened on Aug 29, 2026

• Pooled run_dada is not uniform: occupancy climbs 22 -> 42 cores across a run, and the serial fraction is concentrated in the early rounds

  HPCBio/dada2-rs#152 · Filter by author cjfields opened on Aug 18, 2026
  5

• b_compare's map is slower on reused memory than on freshly-faulted memory (~11-16% of busy); mechanism unresolved, no perf counters available

  HPCBio/dada2-rs#151 · Filter by author cjfields opened on Aug 18, 2026
  1

• b_compare slower per comparison under the #139 carry on soil 16S (likely #151's buffer-reuse effect); re-measure on current main with length-normalized input

  low priority
  HPCBio/dada2-rs#142 · Filter by author cjfields opened on Aug 16, 2026
  4

• Cover binned-qual (and noqual) in walkthroughs, benchmarking, and R concordance

  HPCBio/dada2-rs#120 · Filter by author cjfields opened on Aug 3, 2026
  6

• Test sequence-space density as a predictor of errfun sensitivity (matched abundance strata)

  low priority
  HPCBio/dada2-rs#118 · Filter by author cjfields opened on Aug 2, 2026

• Is full pooling worth it at scale? Measure dada-pooled vs dada-pseudo on a large diverse run

  experiment
  HPCBio/dada2-rs#106 · Filter by author cjfields opened on Jul 30, 2026
  1