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Reads: yeast panels (Saccharomyces sensu stricto, Candida albicans, Zygosaccharomyces, Lachancea and others) withheld in wave 2 #196
Description
State
- Median flank depth below 2x for S. eubayanus (1.8), S. paradoxus (1.5), S. pastorianus (2.1), S. mikatae (1.3); S. uvarum typed 14 of 20 runs at flank depth 1.6. Cause not examined (hybrids, a panel from few loci, flank divergence are possibilities).
- C. albicans:
bothin 40% of runs, 2 of 5 assembly comparisons agree. Most isolates are a/alpha heterozygous diploids, sobothis expected for a different reason than in Reads: species where presence of an idiomorph cannot be typed (silent cassettes, homothallic, switching) and what the gate should say #195. - 16 species had no panel built: Candida dubliniensis, C. viswanathii, Debaryomyces hansenii, Kluyveromyces lactis, Lachancea fermentati, L. thermotolerans, Lodderomyces orthopsilosis, Schizosaccharomyces japonicus, Zygosaccharomyces bailii, favi, mellis, parabailii, pseudobailii, rouxii, sapae, siamensis (reason not examined).
Dependencies
Only the Ogataea and Pichia panels depend on #188 and #189 (routing and the missing Pichia reference). The Saccharomyces and C. albicans genomes are not phylum-fallback genomes. The silent-cassette problem in #195 applies to the Saccharomyces / Kluyveromyces / Lachancea / Zygosaccharomyces group and decides whether presence panels are meaningful there.
Proposed
- Diagnose the 16 panel failures and the five Saccharomyces holds (a TSV with cause class, as in Reads: work list for the withheld filamentous and other non-yeast species (waves 1 and 2) #194).
- Rebuild a/alpha panels from curated tier A/A1 DB records as well as assembly loci where this helps.
- For heterozygous diploids, keep
bothexpected but do not treat it as a validation; add a junction or ratio test (see Reads: species where presence of an idiomorph cannot be typed (silent cassettes, homothallic, switching) and what the gate should say #195).
Acceptance
Simulated a+alpha mixes per rebuilt panel (minor allele detected at 10% or more share, 3 of 3 replicates) before promotion; S. cerevisiae stays skipped by design.
Activity
hyphaltip commentedon Nov 8, 2026
Status (2026-11-07, reads session; work in PR #283 and #282):
Done:
Not done:
These depend on the panel design in #195, which the curator deferred on 2026-11-07. Leaving open.
hyphaltip commentedon Nov 9, 2026
Curator ruling 2026-11-09 (design note in PR #321): this issue closes for v0.9.0 when these merge.
panel_build_failedspecies (Zygosaccharomyces ×8, Lachancea ×3, K. lactis, D. hansenii, C. dubliniensis, C. viswanathii, L. orthopsilosis, S. japonicus);noneat flank depth 1.1–1.9;Moved to v0.10.0: the rebuilt a/alpha panels from curated records, the simulated-mix acceptance, and active-MAT typing (#322 and #323).
Notes: junction-panel and cannot-be-typed design for #195/#196 (propo…
Gate causes (#195/#196): causes.tsv, NOT_TYPABLE:homothallic_locus|si…
Reads gate causes for v0.9.0 (#195, #196): not typable, zygosity, unc…