A near complete genome for goat genetic and genomic research.
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
Goat de-novo genome ASSEMBLY paper (Saanen_v1 = GenBank GCA_015443085.1). The full assembly (PacBio CLR + Hi-C, ~2.69 Gb, thousands of CPU-h) is out of scope; the named code repo IsoSeq is only an annotation-evidence track and the paper reports NO IsoSeq-specific numbers to grade. In-scope 80/20: recompute the published assembly-quality statistics from the DEPOSITED assembly on «our HPC»/«infra» using an independent pure-python streamer, cross-checked against NCBI's own assembly_stats.txt and seqkit. Result: 4 headline numbers reproduce 1:1 EXACT (total length 2.696 Gb = paper 2.69 Gb; contig N50 46,208,332 bp = 46.2 Mb; scaffold N50 102,383,509 bp = 102.3 Mb; chromosomal 2.638 Gb = paper 2.637 Gb) and gaps within-tol (NCBI spanned-gaps 169 = paper exactly; my naive N-run count 170, an off-by-one from gap definition). No fabrication signal — every reported assembly metric is independently re-derivable from the public assembly. BUSCO (reported 94.3%) was NOT completed: 5 jobs hit a parser bug + HTTP 404 in compleasm's busco-data downloader (broken upstream in every version), and the comparison would be approximate-only anyway (paper used BUSCO v3.0.2/mammalia_odb9/protein mode vs a modern genome-mode odb10) — left as optional last-20% per brief. NOT attempted: de-novo reassembly, gene-annotation counts (EvidenceModeler integration), IsoSeq transcript counts (no reported target).
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 89assessed: 2026-06-15 ⛓ 4c3695e94bcb
✎ 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
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🤖 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 high-depth PacBio long-read sequencing combined with Hi-C scaffolding produce a near-complete, high-quality goat reference genome (Saanen_v1)—including continuous X and the first Y chromosome scaffolds—that improves upon the existing ARS1 assembly for goat genetic and genomic research?
- ★ Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold. resource
- ★ Saanen_v1 is more complete than ARS1, with centromeric/telomeric repeats at ends of two-thirds of autosomes, fewer gaps (169 vs 773), and more sequence on chromosomes (2.63 Gb vs 2.58 Gb). finding
- ★ Eight putative large assembly errors (1 to ~7 Mb each) present in ARS1 were identified and amended in Saanen_v1. finding
- ★ Saanen_v1 enables reassignment of likely correct positions for 4.4% of SNP probes in the GoatSNP50 chip. finding
- ★ The substitution rate of the ruminant (goat) Y chromosome was estimated for the first time, allowing estimation of the male-to-female mutation rate ratio. finding
- ★ A combined approach of high-depth PacBio long-read sequencing (117×) plus Hi-C (118×) scaffolding was used to assemble the genome. method
- Y chromosome scaffolds were resolved by selecting the Flye assembly, which contained seven Y-linked single-copy genes in conserved order matching the ovine Y chromosome. method
- Genes were comprehensively annotated combining ab initio, homology-based, and RNA-seq/Iso-Seq-assisted prediction integrated by EvidenceModeler. method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| PacBio long-read (SMRT) whole-genome sequencing | Saanen dairy goat (Capra hircus), male buck, liver tissue DNA | none | long reads / subreads for de novo assembly | PacBio Sequel II, Sequel Binding Kit 1.0, Sequencing Kit 1.0, SMRT Cell 8M |
| Illumina short-read whole-genome sequencing | Saanen dairy goat, same individual, liver DNA | none | paired-end 150 bp reads for polishing and kmer genome-size estimation | Illumina HiSeq X Ten, TruSeq Nano DNA Library Prep Kit |
| Hi-C chromatin conformation capture sequencing | Saanen dairy goat, same individual, blood DNA | MboI restriction digestion / cross-linking | chromatin interaction matrix for scaffolding to chromosome level | Illumina HiSeq X Ten |
| Short-read RNA-seq | goat tissues (publicly available SRA and unpublished Illumina data) | none | transcript evidence for gene annotation and mapping ratio assessment | — |
| PacBio Iso-Seq (long-read RNA sequencing) | testicular tissue of Saanen individual and abomasum tissue of three Shanbei white Cashmere goats | none | full-length transcripts for gene annotation | PacBio Iso-Seq |
| miRNA-seq analysis | goat (nine downloaded NCBI SRA miRNA-seq datasets) | none | known and novel miRNA identification | — |
| Whole-genome alignment / comparative assembly assessment | Saanen_v1 vs ARS1, CHIR_2.0, Oar_rambouillet_v1.0 goat/ruminant assemblies | none | structural variations, large assembly errors, SNP probe positions | — |
| Multiple sequence alignment for substitution rate estimation | cattle, yak, sheep, goat (autosomes and Y chromosome) | none | substitution rates and male-to-female mutation rate ratio (αm) | — |
- ▼ Saanen_v1 has far fewer gaps than ARS1 169 vs 773 gaps
- ▲ More assembled sequence anchored to chromosomes in Saanen_v1 than ARS1 2.63 Gb vs 2.58 Gb
- – Eight large assembly errors in ARS1 amended in Saanen_v1 1 to ~7 Mb each
- – Correct positions assigned for a fraction of GoatSNP50 chip SNP probes 4.4% of SNP probes
- ▲ Flye assembly scaffold contained more conserved Y-linked single-copy genes than Wtdbg2 7 vs 5 of 10 Y-linked genes
- ▲ Polished Flye assembly showed higher BUSCO completeness than Wtdbg2 version 94.0% vs 93.1%
- – Final polished de novo assembly length and contiguity 2.69 Gb, contig N50 34.0 Mb
- – Estimated goat genome size from 17-kmer distribution 2.72 Gb
- count 169 vs. 773 (number of gaps in Saanen_v1 vs ARS1)
- count 2.63 Gb vs. 2.58 Gb (assembled sequence on chromosomes Saanen_v1 vs ARS1)
- other 4.4% (GoatSNP50 chip SNP probes given likely correct positions)
- other 94.0% vs. 93.1% (BUSCO completeness Flye vs Wtdbg2 polished assemblies)
- other 117× (327.7 Gb) (PacBio SMRT long-read coverage)
- other 118× (Hi-C data coverage)
- other contig N50 33.9 Mb vs 35.3 Mb (Flye vs Wtdbg2 contig continuity)
- count 2.72 Gb (estimated goat genome size from 97 Gb Illumina reads, 17-kmer peak at 71×)
Statistical methods review
Model: opusA 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 de novo genome assembly study that is predominantly descriptive and computational rather than inferential. Rather than hypothesis-testing comparisons between experimental groups, the work reports assembly metrics (contig N50, BUSCO completeness, QV, mapping ratios) and uses a single reference individual, with comparisons made against existing assemblies (ARS1, CHIR_2.0, etc.). The one explicitly model-based statistical analysis is phylogenetic estimation of nucleotide substitution rates for autosomes and sex chromosomes, from which a male-to-female mutation rate ratio was derived.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Phylogenetic substitution-rate estimation (maximum-likelihood under the GTR/REV model with 4 rate categories, PHYLOFIT) | substitution rates for autosomes, X and Y chromosomes across cattle, yak, sheep and goat | 1.96 Gb aligned autosomal sequence and 645.1 kb of X-degenerate Y sequence across four species | stated |
| Substitution-model selection (jModelTest) | choosing the best-fitted model (GTR/REV) for the multiple-sequence alignment | — | stated |
| k-mer (17-mer) frequency-based genome-size estimation | genome size of Saanen_v1 from ~97 Gb Illumina reads | one individual; 17-kmer distribution peak at 71× | not stated |
| BUSCO completeness assessment | assembly completeness vs mammalia_odb9 (4,104 single-copy orthologues) | 4,104 orthologues | na |
| Quality value (QV) estimation via FreeBayes substitution calling | per-assembly base accuracy | own WGS data plus 3 downloaded individuals (Asian, European, African) | na |
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Substitution rates and the derived male-to-female mutation ratio (α_m) were reported as single point estimates from PHYLOFIT.↳ Could also: Bootstrap resampling of alignment blocks or reporting a likelihood-based confidence/credible interval around the rate and α_m estimates would also be a standard option. — An interval would convey the uncertainty of the estimate, which is helpful given the restricted X-degenerate region (645.1 kb) used for the Y chromosome.
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Genome size was estimated from a single individual's 17-mer distribution using the peak-depth formula.↳ Could also: Fitting a full k-mer mixture model (e.g., GenomeScope) and/or comparing multiple k lengths would also be a common approach. — A model fit can additionally estimate heterozygosity and repeat content and provide a fitted error envelope around the size estimate.
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Assembly-to-assembly comparisons (continuity, mapping ratios, gene counts) were presented as descriptive metrics for Saanen_v1 versus ARS1 and other references.↳ Could also: Reference-free k-mer based metrics such as Merqury QV/completeness could also be reported alongside the alignment-based QV. — Reference-free metrics avoid dependence on a chosen comparison assembly and offer an independent line of evidence for base accuracy and completeness.
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QV was computed from a small set of individuals (own data plus three downloaded genomes spanning Asian, European and African origins).↳ Could also: Summarizing the per-individual QV values with a mean and a measure of spread (range or SD) across the datasets would also be an option. — Showing the spread across individuals would communicate how consistent the accuracy estimate is across genetic backgrounds.
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Model selection relied on jModelTest choosing GTR/REV with four rate categories.↳ Could also: Reporting the information-criterion (AIC/BIC) values for the candidate models, or a sensitivity check under an alternative model, would also be standard practice. — Documenting the selection criteria and a robustness check shows how much the downstream rate estimates depend on the chosen model.
Result convergence & founder nodes
Findings this paper shares with others that ran a comparable experiment. A node’s strength is how many independent papers report it (replication breadth) — not how often it is cited, so a heavily-replicated but under-cited founder still stands out.
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Saanen_v1 anchors more assembled sequence to chromosomes (2.63 Gb) than ARS1 (2.58 Gb) via Hi-C scaffolding.Hi-C capra hircus up 2021×1papers★ This paper is the founder (earliest)
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Flye-based Y-chromosome scaffold recovers more conserved Y-linked single-copy genes (7/10) than the Wtdbg2 scaffold (5/10).long-read-DNA capra hircus y-chromosome up 2021×1papers★ This paper is the founder (earliest)
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Eight large structural assembly errors (1–7 Mb each) present in ARS1 are corrected in the Saanen_v1 assembly.long-read-DNA capra hircus 2021×1papers★ This paper is the founder (earliest)
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Saanen_v1 contains far fewer assembly gaps (169) than the ARS1 reference assembly (773).long-read-DNA capra hircus down 2021×1papers★ This paper is the founder (earliest)
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Polished Flye assembly has higher BUSCO completeness (94.0%) than the Wtdbg2 assembly (93.1%).long-read-DNA capra hircus up 2021×1papers★ This paper is the founder (earliest)
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Saanen_v1 de novo assembly spans 2.69 Gb with a contig N50 of 34.0 Mb, constituting a near-complete goat reference genome.long-read-DNA capra hircus 2021×1papers★ This paper is the founder (earliest)
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4.4% of GoatSNP50 chip SNP probes map to corrected positions in Saanen_v1 relative to ARS1, indicating prior misassembly.other capra hircus 2021×1papers★ This paper is the founder (earliest)
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Saanen goat genome size is estimated at 2.72 Gb by 17-mer k-mer frequency distribution of Illumina reads.WGS capra hircus 2021×1papers★ This paper is the founder (earliest)
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.
This is a genome-assembly paper (Saanen_v1 goat reference, GenBank
GCA_015443085.1_Saanen_v1). The full de-novo assembly (PacBio CLR + Hi-C of a
2.69 Gb genome; Flye/Wtdbg2/MECAT2/Racon/Pilon/3D-DNA/PBjelly) is out of scope
(thousands of CPU-hours, the heavy "last 20%++").
In scope (deterministic, gradeable): the published assembly-quality statistics, recomputed from the deposited assembly FASTA:
- Total length 2.69 Gb (ungapped 2.637 Gb)
- Contig N50 46.2 Mb
- Scaffold N50 102.3 Mb
- Number of gaps 169
Secondary (named pipeline tool, approximate): BUSCO completeness. Paper reports 94.3 % with BUSCO v3.0.2, mammalia_odb9 (4,104 orthologues), protein mode. We run a modern genome-mode completeness check (compleasm / mammalia_odb10) as an audit cross-check — mode + DB differ, so this is an approximate comparison.
Named code repo is PacBio IsoSeq (v3.2.2) used for transcript evidence in annotation, but the paper reports no IsoSeq-specific numbers (CCS/FLNC/isoform counts) in the text or tables — nothing to grade against — so a bare IsoSeq run is not a useful reproduction target and is documented as such rather than run.
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.
This goat genome-assembly paper reproduces exactly: all four published assembly-quality statistics (total length 2.69 Gb, chromosomal 2.637 Gb, contig N50 46.2 Mb, scaffold N50 102.3 Mb) are independently re-derivable from the deposited GenBank assembly and agree to reported precision across a custom Python streamer, NCBI's own stats, and seqkit. The only deviation is a definitional off-by-one in gap counting (naive 170 vs NCBI spanned-gap 169, the latter matching the paper exactly). BUSCO completeness (94.3%) was not finished, but solely due to upstream tool/server breakage and it would have been an approximate cross-check anyway — neither an authors' nor a data-availability defect. No fabrication signal; the central claim of a near-complete reference holds.
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.