Issues

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

  enhancement
  HPCBio/dada2-rs#246 · Filter by author cjfields opened on Sep 30, 2026
  1

• 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

  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

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

• Concordance: run_illumina.sh cannot pin the error-model training set, and has no nbases guard

  enhancement
  HPCBio/dada2-rs#225 · 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
  1

• Conciseness review

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

• experiment: measure the member-order reproducibility floor (Bi::raws permutation sensitivity)

  HPCBio/dada2-rs#157 · Filter by author cjfields opened on Aug 29, 2026
  4

• 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

• b_compare costs 1.3-1.65x more per comparison under the #139 carry on soil 16S; unexplained, and paid for many times over

  HPCBio/dada2-rs#142 · Filter by author cjfields opened on Aug 16, 2026
  3

• 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

• filter-and-trim: no primer-sequence-aware trimming; fixed --trim-left cannot handle heterogeneity spacers

  low priority
  HPCBio/dada2-rs#113 · Filter by author cjfields opened on Aug 1, 2026
  1

• merge-pairs: input-provenance warning fires on every sample when dada was run from derep JSON

  HPCBio/dada2-rs#111 · Filter by author cjfields opened on Aug 1, 2026

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

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

• Diagnostics for error-model fit: per-sample deviation and model calibration

  HPCBio/dada2-rs#105 · Filter by author cjfields opened on Jul 30, 2026
  1

• Tabular roll-up of per-sample run metrics (unique fraction, reads through pipeline)

  HPCBio/dada2-rs#104 · Filter by author cjfields opened on Jul 30, 2026
  1

• Reorganize the test suite: file layout, shared scaffolding, and core-module coverage

  enhancementlow priority
  HPCBio/dada2-rs#103 · Filter by author cjfields opened on Jul 29, 2026

• Binned quality: compare loess vs binned-qual vs pacbio error profiles, and guard against a mismatched errfun

  HPCBio/dada2-rs#98 · Filter by author cjfields opened on Jul 26, 2026
  7