A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- Every checked point held up.
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
REPRODUCED (1:1, provisional). De-Kayne et al. 2025, haplotype-resolved bocaccio rockfish genome (J Hered). Described well enough to reproduce: public CCGP/VGP-style pipeline and two public deposited assemblies. Strategy (BRIEF P16): ran standard third-party QC tools on the paper's own deposited data products and compared 1:1 to Table 2. All 14 in-scope QC metrics regenerated on «our HPC» — 13 exact, 1 within-tolerance. gfastats v1.3.11 reproduced every contiguity number to the base pair for both haplotypes (total length, #scaffolds, scaffold N50, largest scaffold, #contigs, contig N50). BUSCO 5.8.2 (actinopterygii_odb10, n=3640) reproduced hap1 completeness exactly and hap2 to a single BUSCO (Fragmented 0.5% vs 0.6%; C/S/D/M identical). The deposited genomes faithfully match the published QC table — no sign of fabrication. NOT attempted (hard ~20%, by design): re-running hifiasm from raw PRJNA720569 reads, merqury QV (64.5533) / k-mer completeness (97.33%), repeat content (45.66%), MitoHiFi mitogenome, GenomeScope size/heterozygosity. A prior session ended as a VPN-only error (no compute); this re-run completed cleanly with «our HPC» reachable throughout.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 99assessed: 2026-06-20 ⛓ ce76c73f81fe
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-20
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-20no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnet- ★ This paper presents the first de novo, haplotype-resolved reference-quality genome assembly of Sebastes paucispinis (bocaccio rockfish). resource
- ★ The genome was assembled using PacBio HiFi long reads combined with Omni-C (Hi-C) proximity-ligation data via the CCGP assembly pipeline (HiFiasm contiging, SALSA scaffolding, manual curation with Omni-C contact maps). method
- ★ The resulting diploid assembly is highly contiguous and complete, with two phased haplotype assemblies of similar size (~807 Mb and ~803 Mb). finding
- Repeat content and transposable element diversity across the S. paucispinis genome were characterized using a species-specific repeat library combined with Dfam ancestral repeats. finding
- ★ The genome resource is intended to support conservation genomics of bocaccio, a species that declined ~96-98% due to historical overfishing and was federally declared overfished in 2005. resource
- Assembly completeness was validated by BUSCO comparison against other Sebastes rockfish genome assemblies (S. entomelas, S. fasciatus, S. umbrosus). method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| PacBio HiFi long-read sequencing | Sebastes paucispinis liver tissue (single specimen, SEB-726) | none | Genome sequence reads, read length distribution, sequencing coverage | PacBio Sequel IIe with SMRTbell Express Template Prep Kit v2.0 |
| Omni-C (Hi-C) proximity ligation sequencing | Sebastes paucispinis liver tissue (same individual) | none | Chromatin contact pairs for scaffolding and contact map generation | Illumina NovaSeq 6000, Dovetail Omni-C Kit |
| K-mer analysis / genome profiling | Sebastes paucispinis genomic DNA (HiFi reads) | none | Genome size, heterozygosity, repeat content estimates | Meryl (k=21) and GenomeScope 2.0 |
| De novo genome assembly and scaffolding | Sebastes paucispinis HiFi reads + Omni-C reads | none | Phased haplotype contigs and scaffolds | HiFiasm (Hi-C mode), SALSA, Rapid Curation pipeline, YAGCloser |
| Genome completeness assessment (BUSCO) | Assembled S. paucispinis genome (haplotype 1 and 2) | none | Percentage of complete single-copy orthologs | BUSCO v5.8.2, actinopterygii_odb10 database |
| Base-level accuracy and k-mer completeness assessment | Assembled S. paucispinis genome + HiFi meryl database | none | QV (Phred base accuracy) and k-mer completeness | Merqury |
| Repeat/transposable element annotation | Assembled S. paucispinis genome | none | Repeat element classes and genome proportion masked | RepeatModeler, Dfam, CD-HIT, RepeatMasker v4.1.2-p1 |
| Contamination screening | Assembled S. paucispinis genome | none | Taxonomic assignment of scaffolds / contaminant detection | BLAST+ v2.15 (nt database), BlobToolKit v2.3.3 |
- – Haplotype 1 assembly (fSebPau1.0.hap1) spans 806.86 Mb across 211 scaffolds with contig N50 14.26 Mb and scaffold N50 34.62 Mb. 806.86 Mb, N50 14.26 Mb/34.62 Mb
- – Haplotype 2 assembly (fSebPau1.0.hap2) spans 802.85 Mb across 115 scaffolds with contig N50 18.44 Mb and scaffold N50 43.52 Mb. 802.85 Mb, N50 18.44 Mb/43.52 Mb
- – GenomeScope 2.0 estimated genome size of 767.83 Mb with 0.211% heterozygosity and 0.153% sequencing error rate. 767.83 Mb; 0.211% het
- – PacBio HiFi sequencing yielded ~79x genome coverage with mean read length 13,283 bp (N50 13,699 bp). ~79.95X coverage
- – Overall assembly quality code reported as fSebPau1(7.7.P7.Q64.C99). 7.7.P7.Q64.C99
- – K-mer spectrum showed a bimodal distribution with major coverage peak at ~100-fold and minor peak at ~50-fold, consistent with a diploid, heterozygous genome. peaks at ~100x and ~50x
- – Omni-C library generated 216.72 million read pairs, used for scaffolding and manual curation of both haplotypes. 216.72M read pairs
- count 6.01 million HiFi reads (PacBio HiFi sequencing output)
- other ~79.95X genome coverage (HiFi) (Sequencing depth for assembly)
- other 767.83 Mb estimated genome size; 0.211% heterozygosity; 0.153% error rate (GenomeScope 2.0 k-mer-based genome profiling)
- count 806,866,550 bp (hap1) / 802,857,081 bp (hap2) final assembly size (Final phased haplotype assembly sizes)
- other Contig N50: 14,264,469 bp (hap1) / 18,449,034 bp (hap2) (Assembly contiguity metric)
- other Scaffold N50: 34,620,701 bp (hap1) / 34,476,039 bp (hap2) (Assembly contiguity metric (Table 2))
- count 3,640 genes (Actinopterygii_odb10 BUSCO ortholog database size used for completeness assessment)
- other 216.7 million spots, 65.4 Gb bases, 21.5 Gb (Omni-C Illumina reads) (Omni-C sequencing run statistics)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This paper describes a de novo, haplotype-resolved genome assembly for a single Sebastes paucispinis specimen, built from PacBio HiFi long reads and Dovetail Omni-C proximity-ligation data using a standard long-read assembly and scaffolding pipeline (HiFiasm, SALSA, manual curation). Rather than inferential hypothesis-testing statistics, the paper reports computational/bioinformatic quality-assessment metrics — k-mer-based genome size and heterozygosity estimation (GenomeScope2.0), assembly contiguity statistics (N50/NG50), gene-set completeness (BUSCO), base-level accuracy (Merqury QV), and repeat content (RepeatMasker) — and compares BUSCO completeness descriptively against three other published Sebastes genome assemblies. No p-values, effect sizes, or formal group comparisons are presented.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| k-mer-based genome size, heterozygosity, and error-rate estimation (GenomeScope 2.0) | estimating genome size, heterozygosity, and sequencing error rate from HiFi k-mer spectrum | one specimen's HiFi read set | not stated |
| BUSCO ortholog completeness assessment | genome completeness/functional-completeness evaluation, compared descriptively against S. entomelas, S. fasciatus, and S. umbrosus assemblies | one assembly per haplotype/species, actinopterygii_odb10 (3,640 genes) | not stated |
| Merqury k-mer-based base accuracy (QV) and completeness estimation | assessing base-level accuracy and k-mer completeness of the assembly | one specimen's meryl k-mer database | not stated |
| BUSCO gene-set frameshift analysis (Korlach et al. 2017 pipeline) | further estimating assembly accuracy | one assembly | not stated |
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BUSCO completeness scores for the focal assembly are compared descriptively (as raw percentages) against three other Sebastes assemblies without a formal statistical test.↳ Could also: A proportion-based comparison (e.g., confidence intervals around each completeness percentage, given the fixed ortholog set size) could also be reported. — This would convey the precision of each completeness estimate and make the magnitude of differences between assemblies easier to interpret quantitatively.
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Genome size, heterozygosity, and sequencing error rate are reported as single point estimates from GenomeScope2.0's k-mer model fit.↳ Could also: Reporting the model-fit confidence intervals GenomeScope produces, or performing a bootstrap resampling of the k-mer spectrum, could also be used. — This would communicate the uncertainty inherent in k-mer-based estimation, which can be useful when comparing estimated versus assembled genome size.
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Base-level accuracy (QV) from Merqury is reported as a single value per haplotype.↳ Could also: A confidence interval or standard error around the QV estimate (derivable from the underlying k-mer error model) could also be presented. — This would give readers a sense of how precisely the accuracy value is estimated, particularly useful when comparing QV across haplotypes or assemblies.
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The assembly and all quality metrics are derived from a single specimen.↳ Could also: Where feasible, sequencing and assembling additional individuals (or comparing against population resequencing data) could also be used to distinguish individual-specific variation from species-typical genomic features. — This is a common extension in conservation genomics to contextualize how representative a single reference genome is of the broader population, though single-individual assemblies are the accepted standard for reference genome projects like this one.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-40323688
Paper: De-Kayne et al. 2025, A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis. J Hered. DOI 10.1093/jhered/esaf026. Type: "Genome Resources" note — a single de-novo, haplotype-resolved genome assembly + standard QC.
Code: https://github.com/ccgproject/ccgp_assembly — the CCGP (California Conservation Genomics Project) assembly pipeline. Shell-script modules implementing the Rhie-et-al-2021 VGP-style protocol: HiFiAdapterFilt → hifiasm (Hi-C mode) → purge_dups → SALSA scaffolding → YAGCloser → MitoHiFi → BUSCO/meryl/merqury QC. This is a third-party reusable tool applied to the paper's own data (P16: equally valid to reproduce).
Data: BioProject PRJNA720569 (raw HiFi + Omni-C, SRA). Deposited products:
- hap1 assembly GCA_036937225.1 (fSebPau1.0.hap1)
- hap2 assembly GCA_036937175.1 (fSebPau1.0.hap2)
Reproduction strategy (80/20)
The honest, clear, cheap path that directly tests the paper's headline numbers is to recompute the assembly-evaluation metrics (Table 2) from the deposited assembly FASTAs using standard third-party QC tools, and compare 1:1 to the printed values. This is exactly the fabrication-detection target: do the reported QC numbers match the genome that was actually deposited? The brief explicitly blesses running a third-party tool on the paper's data.
IN SCOPE (attempted — cheap, deterministic, derivable from deposited FASTA)
Pipeline that produced them: the QC stage of ccgp_assembly (gfastats/assembly-stats, BUSCO, GC).
| result | reported (Table 2) | tool to recompute |
|---|---|---|
| hap1 total length | 806,866,550 bp | gfastats / seqkit |
| hap2 total length | 802,857,081 bp | gfastats / seqkit |
| hap1 #scaffolds | 211 | gfastats |
| hap2 #scaffolds | 115 | gfastats |
| hap1 scaffold N50 | 34,620,701 bp | gfastats |
| hap2 scaffold N50 | 34,476,039 bp | gfastats |
| hap1 largest scaffold | 43,679,056 bp | gfastats |
| hap2 largest scaffold | 43,528,066 bp | gfastats |
| hap1 #contigs | 378 | gfastats (split at gaps) |
| hap2 #contigs | 278 | gfastats |
| hap1 contig N50 | 14,264,469 bp | gfastats |
| hap2 contig N50 | 18,449,034 bp | gfastats |
| hap1 BUSCO | C:99.3%[S:98.8%,D:0.5%],F:0.6%,M:0.1% | BUSCO actinopterygii_odb10 (n=3640) |
| hap2 BUSCO | C:99.3%[S:98.9%,D:0.4%],F:0.6%,M:0.1% | BUSCO actinopterygii_odb10 (n=3640) |
OUT OF SCOPE / the hard 20% (NOT attempted — say why)
- Re-running hifiasm from raw reads to regenerate the assembly itself. Requires ~63 Gb HiFi + 216 M Omni-C pairs, multi-day high-mem assembly; result is not byte-identical across hifiasm versions anyway. The deposited assembly IS the paper's data product; recomputing its QC is the faithful, in-budget test.
- QV 64.5533 / k-mer completeness 97.33% — needs merqury with a meryl k-mer DB built from the raw HiFi reads (large download + build). Optional; skipped to keep to a few clear points unless time permits.
- Repeat content 45.66% (RepeatModeler/RepeatMasker) — heavy, stochastic, model- dependent. Out of scope.
- Mitochondrial genome (MitoHiFi), GenomeScope size/heterozygosity, HiFi/Omni-C read-N50 stats — derived from raw reads, not the deposited assembly; out of scope for this pass.
Wet-lab / external (never in scope)
DNA extraction, library prep, sequencing, chromosome count 2n=48 (cytogenetics).
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
Reproduction ran standard QC (gfastats v1.3.11, BUSCO 5.8.2) on the paper's own deposited assemblies (GCA_036937225.1, GCA_036937175.1) and matched 13/14 Table-2 metrics exactly to the base pair. The single within-tolerance item — hap2 BUSCO Fragmented 0.5% vs 0.6% (1 BUSCO of 3640, C/S/D/M identical) — is attributable to BUSCO predictor-version noise, on the technical/expected side. Every reported value is derivable from the shared data with no fabrication concern; the central claim of a high-quality haplotype-resolved genome is fully confirmed. Note the hard ~20% (hifiasm reassembly, merqury QV, repeat content) was out of scope, but the in-scope comparison is a clean 1:1.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.