Chromosome-level genome of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus.
The main results reproduced: recomputed values matched the published ones within tolerance.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡Overall, the reproduction showed a material discrepancy
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
Described well enough to reproduce: YES. Repo is README-only (parameters, no scripts), but assembly (NCBI GCA_036320965.1) + survey reads (SRA SRR26801482) both resolve, so this is reproducible via standard third-party tools on the paper's own data (brief P16). RESULT = 1:1 agreement on the assembly-statistics data point (DP1): all 6 reported metrics match the deposited assembly to <=0.5%, with scaffold N50 (51,049,391 bp) and chromosome count (73) EXACT to the unit -> no evidence of assembly-stat fabrication. This DP1 check used the authoritative NCBI Datasets metadata (control-plane, zero compute), NOT an independent from-FASTA recompute. NOT attempted/blocked: DP2 (k-mer genome survey: KMC k=17 + GenomeScope2 on SRR26801482 to test genome size 2917.34 Mb / heterozygosity 0.92%) was fully scripted and staged for «our HPC» but NOT executed because the «our HPC» VPN tunnel was never established (Cisco SAML 2FA needs the human operator; not completed in the session window before finalize was requested). NOT attempted by design (hard 20%): full de novo assembly (292 Gb PacBio CLR), Hi-C scaffolding (456 Gb + manual Juicebox curation), gene/repeat annotation. FLAG for human: repo README genome-size estimate (2524.70 Mb) disagrees ~16% with the paper text (2917.34 Mb) for the same k-mer survey.
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.
-
v1 current initial assessment Score 80assessed: 2026-06-15 ⛓ d16f600d7bbd
✎ 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
- 2026-06-15
- Rubric version
- v1.0
- Assessed by
-
🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-15no 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: opusCan a high-quality, chromosome-level reference genome be assembled for the endangered ornate spiny lobster (Panulirus ornatus) to support its conservation, population genetics, and comparative crustacean genomics?
- ★ A chromosome-level genome of P. ornatus spanning 2.65 Gb was assembled with a contig N50 of 51.05 Mb, anchoring 99.11% of sequences to 73 chromosomes. resource
- ★ The genome comprises 65.67% repeat sequences. finding
- ★ 22,752 protein-coding genes were predicted, of which 99.20% were functionally annotated. finding
- ★ Integrating Illumina short reads, PacBio long reads, and Hi-C produced the first chromosome-level genome assembly for an endangered lobster species. method
- This assembly markedly improves on a previous fragmented attempt (1.93 Gb assembled, contig N50 of 5,451 bp). finding
- Four types of noncoding RNAs were annotated: 12,771 miRNAs, 5,187 tRNAs, 1,716 rRNAs, and 1,296 snRNAs. finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| WGS short-read sequencing | P. ornatus male adult muscle tissue | none | 182.90 Gb of short reads for genome survey and polishing | Illumina HiSeq 6000 |
| WGS long-read sequencing (PacBio CLR) | P. ornatus muscle tissue | none | 292.02 Gb raw continuous long reads for de novo assembly | PacBio Sequel II (SMRT) |
| Hi-C sequencing/scaffolding | P. ornatus muscle tissue | MboI restriction digestion / cross-linking | 456.71 Gb paired-end reads for chromosome scaffolding | Illumina HiSeq/NovaSeq 6000 |
| RNA-seq (transcriptome) | P. ornatus eight tissues (testis, intestines, hepatopancreas, hemocytes, muscle, gills, heart, eyestalk) | none | 54.38 Gb clean reads for gene structure annotation | Illumina HiSeq 6000; NEBNext Ultra RNA Library Prep Kit |
| K-mer genome survey | P. ornatus Illumina reads | none | estimated genome size, heterozygosity, repeat content | SOAPec v2.01; GenomeScope v2.0 |
- – Final genome assembly size of 2,651,872,113 bp (2.65 Gb) 2.65 Gb
- – Scaffold N50 reached 51.05 Mb in the final assembly 51.05 Mb
- – 2,628.95 Mb anchored to 73 chromosomes, accounting for 99.11% of the assembly 99.11%
- – Repeat sequences constituted 65.67% of the genome 65.67%
- – LINEs accounted for 40.30%, LTRs 30.07%, DNA elements 4.58%, SINEs 0.01% of the genome LINE 40.30%; LTR 30.07%
- – 22,568 of 22,752 predicted genes (99.20%) annotated by at least one database 99.20%
- – Estimated genome size by K-mer survey was 2917.34 Mb with heterozygosity 0.92% and repeat content 63.86% 2917.34 Mb; 0.92%
- – 14 chromosomes assembled with no more than 30 gaps each 14 chromosomes
- count 2,651,872,113 bp total assembly length (Final genome size)
- count 51.05 Mb scaffold N50 (Hi-C assembly continuity)
- count 73 chromosomes (Anchored chromosomes)
- other 99.11% (Proportion of assembly anchored to chromosomes)
- count 22,752 protein-coding genes (Final gene set)
- other 65.67% (Repeat sequence content of genome)
- other 0.92% heterozygosity; 63.86% repeat (Genome survey estimates)
- count K-mer dominant peak depth of 59; estimated 2917.34 Mb (17 K-mer frequencies analyzed in genome survey)
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 is a genome assembly data descriptor reporting no inferential statistical tests; all analyses are computational and descriptive. Genome size (~2.92 Gb estimated, 2.65 Gb assembled) and heterozygosity (0.92%) were estimated by 17-mer K-mer frequency profiling using SOAPec and GenomeScope2. Assembly quality was characterized by contig/scaffold N50 values, total assembled length, and chromosomal anchoring percentages. Gene prediction and functional annotation results were reported as counts and proportions across multiple databases and prediction methods.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| K-mer frequency analysis (17-mer) for genome size and heterozygosity estimation | Genome survey prior to assembly; dominant peak depth of 59 used to estimate genome size at 2,917.34 Mb and heterozygosity at 0.92% | — | not stated |
| BLAST sequence alignment with E-value cutoff 1E-5 | Functional annotation of 22,752 predicted protein-coding genes against SwissProt, NR, KEGG, InterPro, GO, and Pfam databases | 22,752 predicted genes | not stated |
| Kimura two-parameter divergence calculation for transposable elements | TE landscape characterization to show divergence rate distribution (Fig. 4) using calcDivergenceFromAlign.pl and createRepeatLandscape.pl | — | not stated |
-
Assembly completeness was characterized by N50 values and total assembled length; no standardized gene-space completeness benchmarking tool (e.g., BUSCO) was mentioned in the provided text↳ Could also: BUSCO (Benchmarking Universal Single-Copy Orthologs) assessed against an arthropod or metazoan lineage database — BUSCO provides a universally comparable completeness metric — the proportion of expected conserved single-copy genes recovered — that complements contiguity metrics like N50 and enables direct, standardized comparison across assemblies from different species and studies
-
Genome size and heterozygosity were estimated using a single K value (17-mer) with SOAPec and GenomeScope2↳ Could also: K-mer profiling at multiple values (e.g., 17, 21, 31-mer) with cross-validation, or Smudgeplots alongside GenomeScope2 — Comparing estimates across K values helps assess the robustness of the size and heterozygosity estimates; Smudgeplots additionally infer ploidy level from K-mer pair coverages, which can be informative when heterozygosity is non-negligible (here 0.92%)
-
Two long-read assemblers (Wtdbg2 and Flye) were run independently and their outputs merged with Quickmerge↳ Could also: Hifiasm or Canu could serve as primary or secondary assemblers in a dual-assembler strategy; Hifiasm also supports native Hi-C phasing — Hifiasm is optimized for PacBio CLR/HiFi data and frequently achieves high contiguity; its built-in Hi-C phasing mode can produce haplotype-resolved assemblies in a single workflow, which may be relevant given the observed heterozygosity
-
Assembly polishing was performed with two rounds of Arrow (PacBio-based consensus) followed by two rounds of Pilon (Illumina short-read based)↳ Could also: HyPo, NextPolish, or Medaka as alternative polishing tools, applied sequentially or in place of one of the Pilon rounds — HyPo has been shown to achieve high per-base accuracy with fewer computational resources and iterations; benchmarking polishing tools on the draft assembly can identify the approach that minimizes residual errors for a given genome and read set
-
Gene prediction integrated five de novo tools, nine homology sources, and RNA-seq evidence via EvidenceModeler, with manual PASA update↳ Could also: MAKER2 or BRAKER2 (with AUGUSTUS and GeneMark) pipelines could also integrate these evidence types in a unified, reproducible framework — MAKER2 produces standardized Annotation Edit Distance (AED) scores for each predicted gene model, providing an objective, per-gene quality metric alongside the aggregate annotation statistics reported here
-
The reference genome was assembled from a single male individual with no additional individuals sequenced↳ Could also: Trio-binning (using parental short reads) or Hi-C-phased assembly with Hifiasm could produce a fully phased, haplotype-resolved diploid assembly from the same single individual — Single-individual assemblies are the standard approach for reference genome projects; however, given the 0.92% heterozygosity estimated for this species, a phased assembly would additionally capture allelic variation at the chromosome scale, which could be informative for downstream population genomics studies
Citation network
Where this publication sits in the reproducibility-weighted citation graph — what it is built on, and what is built on it. Citation data from OpenAlex.
No assessed neighbours yet — the network grows as more papers are assessed.
Data lineage
The datasets this paper uses (text-mined from the full text via Europe PMC), and which other assessed papers stand on the same data. A shared dataset is a factual link — not a judgement.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-38909031
Paper: Ren et al. 2024, Sci Data — Chromosome-level genome of the ornate spiny lobster Panulirus ornatus. DOI 10.1038/s41597-024-03512-9. PMCID PMC11193758. Repo: github.com/sundongfang/Chromosome-level-genome-of-Panulirus-ornatus — README only (parameter list, no runnable scripts). Per brief P16, applying standard third-party tools to the paper's own data is an equally valid reproduction. Assembly: NCBI GCA_036320965.1 (ASM3632096v1). Survey reads: SRR26801482 (Illumina WGS PE150, ~93.8 Gbp). BioProject PRJNA1036297.
In scope (attempted)
| result | pipeline | feasibility | data point |
|---|---|---|---|
| Assembly total length, scaffold N50, contig N50, #scaffolds, #chromosomes, max contig, GC | recompute directly from published assembly FASTA (seqkit/assembly-stats) | LIGHT — download ~0.8 GB, minutes | DP1 |
| Genome-survey size, heterozygosity, repeat % | k-mer count (KMC k=17) + GenomeScope2 on SRR26801482 | MEDIUM — ~46 GB download + k-mer count | DP2 |
| BUSCO completeness | BUSCO arthropoda on assembly | optional — version mismatch (paper used odb9/BUSCO v3; modern = odb10/v5), so not 1:1 | DP3 (if time) |
Out of scope (NOT attempted — too heavy or wet-lab/external)
- Full de novo assembly (Wtdbg2/Flye + Arrow + Quickmerge + Pilon on 292 Gb PacBio CLR): hundreds of CPU-days, TB of data. Outside 80/20.
- Hi-C scaffolding (Juicer + 3D-DNA on 456 Gb Hi-C): very heavy, manual Juicebox curation step is non-deterministic.
- Gene annotation (Augustus/Trinity/PASA/EVM → 22,752 genes), repeat annotation (65.67%), ncRNA, functional annotation: multi-tool pipelines, days of compute, many unpinned params.
- DNA extraction / sequencing / karyotype: wet-lab, not computational.
Rationale
DP1 is a deterministic recomputation of reported assembly metrics from the exact published assembly — the cleanest possible 1:1 check and a direct fabrication test. DP2 reproduces the genome-survey pipeline (the only k-mer step) on the paper's own reads with the named tool family (GenomeScope2 v2.0, k=17). Both are clearly specified and low-cost; the assembly/annotation pipelines are the optional hard 20% and are explicitly skipped.
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.
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.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
🚩 Report an error in this record
Spotted something wrong — a verdict you’d contest, a data or value error, or a private detail that slipped through? Tell us, with a short justification. Authors and readers are equally welcome to write in; we review every report.
Prefer email, or the form below not working? Contact us at support@doesitreproduce.com.
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.