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Detail key findings in ReadTheDocs.

Status: Open.

#88 In HPCBio/dada2-rs;

· cjfields opened on Jul 15, 2026

Explore reducing the b_shuffle serial phase (now the dominant pooled-dada bottleneck) — likely a redesign [low priority]

low priorityLower priority tickets; good to check but not necessaryLower priority tickets; good to check but not necessary

Status: Open.

#87 In HPCBio/dada2-rs;

· cjfields opened on Jul 15, 2026

LOESS crate testing

Status: Open.

#84 In HPCBio/dada2-rs;

· cjfields opened on Jul 13, 2026

Housekeeping: reorganize commands into categories

Status: Open.

#83 In HPCBio/dada2-rs;

· cjfields opened on Jul 13, 2026

Carry derep provenance into dada output for robust derep↔dada linkage

Status: Open.

#76 In HPCBio/dada2-rs;

· cjfields opened on Jul 10, 2026

learn-errors: cross-sample diversity in nbases accumulation (sample-level, --randomize doesn't spread reads)

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Open.

#68 In HPCBio/dada2-rs;

· cjfields opened on Jul 9, 2026

Follow-up: reorganize main.rs command dispatch and split cli.rs

Status: Open.

#67 In HPCBio/dada2-rs;

· cjfields opened on Jul 9, 2026

Refine chimera-diagnostics (higher-order/trimera screening) and validate against truth set

Status: Open.

#55 In HPCBio/dada2-rs;

· cjfields opened on Jun 19, 2026

Optimize the WFA backend on long (PacBio) reads

Status: Open.

#51 In HPCBio/dada2-rs;

· cjfields opened on Jun 19, 2026

Evaluate alignment paradigms that solve the global problem differently (pair-HMM, WFA)

Status: Open.

#49 In HPCBio/dada2-rs;

· cjfields opened on Jun 18, 2026

experiment: raise k-mer cap above 8 — are the extra ASVs real? (needs mock-community truth set)

Status: Open.

#44 In HPCBio/dada2-rs;

· cjfields opened on Jun 17, 2026

perf: MiSeq pooled dada under-utilizes cores — serial bud/shuffle/p_update (Amdahl), parallelize

Status: Open.

#33 In HPCBio/dada2-rs;

· cjfields opened on Jun 11, 2026