{"doi":"10.1038/s41586-021-03451-0","title":"Towards complete and error-free genome assemblies of all vertebrate species","abstract":"Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.","journal":"Nature","year":2021,"id":144970,"datarank":6.00710846885765,"base_score":8.057060681965766,"endowment":8.057060681965766,"self_citation_contribution":1.208559102294865,"citation_network_contribution":4.798549366562785,"self_endowment_contribution":1.208559102294865,"citer_contribution":4.798549366562785,"corpus_percentile":96.72004332018257,"corpus_rank":425,"citation_count":3155,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6651,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":15623,"name":"Shane A McCarthy","orcid":"0000-0002-2715-4187","position":1,"is_corresponding":false},{"id":30838,"name":"Olivier Fédrigo","orcid":"0000-0002-6450-7551","position":2,"is_corresponding":false},{"id":24579,"name":"Joana Damas","orcid":"0000-0003-4857-2510","position":3,"is_corresponding":false},{"id":21287,"name":"Giulio Formenti","orcid":"0000-0002-7554-5991","position":4,"is_corresponding":false},{"id":2118,"name":"Sergey Koren","orcid":"0000-0002-1472-8962","position":5,"is_corresponding":false},{"id":550050,"name":"Marcela Uliano‐Silva","orcid":"0000-0001-6723-4715","position":6,"is_corresponding":false},{"id":2108,"name":"William Chow","orcid":"0000-0002-9056-201X","position":7,"is_corresponding":false},{"id":49023,"name":"Arkarachai Fungtammasan","orcid":"0000-0003-2398-0358","position":8,"is_corresponding":false},{"id":551124,"name":"Juwan Kim","orcid":null,"position":9,"is_corresponding":false},{"id":21310,"name":"Chul Lee","orcid":"0000-0002-9403-0774","position":10,"is_corresponding":false},{"id":550053,"name":"Byung June Ko","orcid":"0000-0002-5683-7438","position":11,"is_corresponding":false},{"id":19738,"name":"Mark J. P. Chaisson","orcid":"0000-0001-5395-1457","position":12,"is_corresponding":false},{"id":550051,"name":"Gregory Gedman","orcid":"0000-0001-6819-2019","position":13,"is_corresponding":false},{"id":550052,"name":"Lindsey Cantin","orcid":"0000-0001-9715-533X","position":14,"is_corresponding":false},{"id":2130,"name":"Françoise Thibaud‐Nissen","orcid":"0000-0003-4957-7807","position":15,"is_corresponding":false},{"id":24475,"name":"Leanne Haggerty","orcid":"0000-0001-8843-3596","position":16,"is_corresponding":false},{"id":55988,"name":"Iliana Bista","orcid":"0000-0002-6155-3093","position":17,"is_corresponding":false},{"id":292982,"name":"Michelle Smith","orcid":"0000-0001-5288-0001","position":18,"is_corresponding":false},{"id":550054,"name":"Bettina Haase","orcid":"0000-0001-8945-7282","position":19,"is_corresponding":false},{"id":30895,"name":"Jacquelyn Mountcastle","orcid":"0000-0003-1078-4905","position":20,"is_corresponding":false},{"id":74514,"name":"Sylke Winkler","orcid":"0000-0002-0915-3316","position":21,"is_corresponding":false},{"id":24525,"name":"Sadye Paez","orcid":null,"position":22,"is_corresponding":false},{"id":35642,"name":"Jason T. Howard","orcid":"0000-0003-3265-5127","position":23,"is_corresponding":false},{"id":550055,"name":"Sonja C. Vernes","orcid":"0000-0003-0305-4584","position":24,"is_corresponding":false},{"id":550056,"name":"Tanya M. Lama","orcid":"0000-0002-7372-8081","position":25,"is_corresponding":false},{"id":85910,"name":"Frank Grützner","orcid":"0000-0002-3088-7314","position":26,"is_corresponding":false},{"id":29181,"name":"Wesley C. Warren","orcid":"0000-0003-2255-2730","position":27,"is_corresponding":false},{"id":226126,"name":"Christopher N. Balakrishnan","orcid":"0000-0002-0788-0659","position":28,"is_corresponding":false},{"id":54351,"name":"David W. Burt","orcid":"0000-0002-9991-1028","position":29,"is_corresponding":false},{"id":550057,"name":"Julia M. George","orcid":"0000-0001-6194-6914","position":30,"is_corresponding":false},{"id":21292,"name":"Matthew  T. Biegler","orcid":"0000-0003-4331-9890","position":31,"is_corresponding":false},{"id":551126,"name":"David Iorns","orcid":null,"position":32,"is_corresponding":false},{"id":550058,"name":"Andrew Digby","orcid":"0000-0002-1870-8811","position":33,"is_corresponding":false},{"id":551127,"name":"Daryl Eason","orcid":null,"position":34,"is_corresponding":false},{"id":226099,"name":"Bruce C. Robertson","orcid":"0000-0002-5348-2731","position":35,"is_corresponding":false},{"id":231641,"name":"Taylor Edwards","orcid":"0000-0002-7235-6175","position":36,"is_corresponding":false},{"id":441984,"name":"Mark Wilkinson","orcid":"0000-0002-9459-8976","position":37,"is_corresponding":false},{"id":550059,"name":"George F. Turner","orcid":"0000-0003-0099-7261","position":38,"is_corresponding":false},{"id":237379,"name":"Axel Meyer","orcid":"0000-0002-0888-8193","position":39,"is_corresponding":false},{"id":550060,"name":"Andreas F. Kautt","orcid":"0000-0001-7792-0735","position":40,"is_corresponding":false},{"id":298367,"name":"Paolo Franchini","orcid":"0000-0002-8184-1463","position":41,"is_corresponding":false},{"id":505082,"name":"H. William Detrich","orcid":"0000-0002-0783-4505","position":42,"is_corresponding":false},{"id":503089,"name":"Hannes Svardal","orcid":"0000-0001-7866-7313","position":43,"is_corresponding":false},{"id":550061,"name":"Maximilian Wagner","orcid":"0000-0002-0949-8410","position":44,"is_corresponding":false},{"id":550062,"name":"Gavin J. P. Naylor","orcid":"0000-0002-8731-2626","position":45,"is_corresponding":false},{"id":550063,"name":"Martin Pippel","orcid":"0000-0002-8134-5929","position":46,"is_corresponding":false},{"id":550064,"name":"Milan Malinsky","orcid":"0000-0002-1462-6317","position":47,"is_corresponding":false},{"id":550065,"name":"Mark P. Mooney","orcid":"0000-0002-1943-9967","position":48,"is_corresponding":false},{"id":551128,"name":"Maria Simbirsky","orcid":null,"position":49,"is_corresponding":false},{"id":550066,"name":"Brett T. Hannigan","orcid":"0000-0003-0934-1015","position":50,"is_corresponding":false},{"id":109452,"name":"Trevor Pesout","orcid":"0000-0002-1443-7970","position":51,"is_corresponding":false},{"id":51340,"name":"Marlys L. Houck","orcid":"0000-0002-3879-9511","position":52,"is_corresponding":false},{"id":551129,"name":"Ann Misuraca","orcid":null,"position":53,"is_corresponding":false},{"id":251206,"name":"Sarah B. Kingan","orcid":"0000-0002-4900-0189","position":54,"is_corresponding":false},{"id":77524,"name":"Richard Hall","orcid":"0000-0001-6490-8227","position":55,"is_corresponding":false},{"id":251205,"name":"Zev Kronenberg","orcid":"0000-0002-7627-9808","position":56,"is_corresponding":false},{"id":49038,"name":"Ivan Sović","orcid":"0000-0002-5900-4319","position":57,"is_corresponding":false},{"id":550067,"name":"Christopher Dunn","orcid":"0000-0002-0601-3254","position":58,"is_corresponding":false},{"id":550068,"name":"Zemin Ning","orcid":"0000-0003-4359-776X","position":59,"is_corresponding":false},{"id":251207,"name":"Alex Hastie","orcid":"0000-0002-6401-5864","position":60,"is_corresponding":false},{"id":92298,"name":"Joyce Lee","orcid":"0000-0002-3492-1102","position":61,"is_corresponding":false},{"id":92301,"name":"Siddarth Selvaraj","orcid":null,"position":62,"is_corresponding":false},{"id":7649,"name":"Richard E. Green","orcid":"0000-0003-0516-5827","position":63,"is_corresponding":false},{"id":30066,"name":"Nicholas H. Putnam","orcid":"0000-0002-1315-782X","position":64,"is_corresponding":false},{"id":498871,"name":"Marta Gut","orcid":"0000-0002-4063-7159","position":65,"is_corresponding":false},{"id":92293,"name":"Jay Ghurye","orcid":"0000-0003-1381-4081","position":66,"is_corresponding":false},{"id":109462,"name":"Erik Garrison","orcid":"0000-0003-3821-631X","position":67,"is_corresponding":false},{"id":65853,"name":"Ying Sims","orcid":"0000-0003-4765-4872","position":68,"is_corresponding":false},{"id":2109,"name":"Joanna Collins","orcid":"0000-0001-5782-5028","position":69,"is_corresponding":false},{"id":2112,"name":"Sarah Pelan","orcid":"0000-0001-8729-685X","position":70,"is_corresponding":false},{"id":2115,"name":"James Torrance","orcid":"0000-0002-6117-8190","position":71,"is_corresponding":false},{"id":92288,"name":"Alan Tracey","orcid":"0000-0002-4805-9058","position":72,"is_corresponding":false},{"id":2132,"name":"Jonathan M. D. Wood","orcid":"0000-0002-7545-2162","position":73,"is_corresponding":false},{"id":616410,"name":"Robel E. Dagnew","orcid":null,"position":74,"is_corresponding":false},{"id":550069,"name":"Dengfeng Guan","orcid":"0000-0002-6376-3940","position":75,"is_corresponding":false},{"id":550070,"name":"Sarah E. London","orcid":"0000-0002-7839-2644","position":76,"is_corresponding":false},{"id":550071,"name":"David F. Clayton","orcid":"0000-0002-6395-3488","position":77,"is_corresponding":false},{"id":323738,"name":"Claudio V. Mello","orcid":"0000-0002-9826-8421","position":78,"is_corresponding":false},{"id":550072,"name":"Samantha R. Friedrich","orcid":"0000-0003-0570-6080","position":79,"is_corresponding":false},{"id":323734,"name":"Peter V. Lovell","orcid":"0000-0002-6111-9131","position":80,"is_corresponding":false},{"id":550073,"name":"Ekaterina Osipova","orcid":"0000-0002-6769-7223","position":81,"is_corresponding":false},{"id":550074,"name":"Farooq O. Al-Ajli","orcid":"0000-0002-4692-7106","position":82,"is_corresponding":false},{"id":21322,"name":"Simona Secomandi","orcid":"0000-0001-8597-6034","position":83,"is_corresponding":false},{"id":550075,"name":"Heebal Kim","orcid":"0000-0003-3064-1303","position":84,"is_corresponding":false},{"id":550076,"name":"Constantina Theofanopoulou","orcid":"0000-0003-2014-7563","position":85,"is_corresponding":false},{"id":51339,"name":"Michael Hiller","orcid":"0000-0003-3024-1449","position":86,"is_corresponding":false},{"id":550077,"name":"Yang Zhou","orcid":"0000-0003-1247-5049","position":87,"is_corresponding":false},{"id":19563,"name":"Robert S. Harris","orcid":"0000-0001-5464-6892","position":88,"is_corresponding":false},{"id":19591,"name":"Kateryna D. Makova","orcid":"0000-0002-6212-9526","position":89,"is_corresponding":false},{"id":53921,"name":"Paul Medvedev","orcid":"0000-0003-3143-594X","position":90,"is_corresponding":false},{"id":107646,"name":"Jinna Hoffman","orcid":null,"position":91,"is_corresponding":false},{"id":21312,"name":"Patrick Masterson","orcid":"0000-0001-8837-3706","position":92,"is_corresponding":false},{"id":89204,"name":"Karen Clark","orcid":"0000-0003-4403-1477","position":93,"is_corresponding":false},{"id":24505,"name":"Fergal J. Martin","orcid":"0000-0002-1672-050X","position":94,"is_corresponding":false},{"id":59120,"name":"Kevin L Howe","orcid":"0000-0002-1751-9226","position":95,"is_corresponding":false},{"id":105371,"name":"Paul Flicek","orcid":"0000-0002-3897-7955","position":96,"is_corresponding":false},{"id":4363,"name":"Brian P. Walenz","orcid":"0000-0001-8431-1428","position":97,"is_corresponding":false},{"id":550078,"name":"Woori Kwak","orcid":"0000-0003-0600-067X","position":98,"is_corresponding":false},{"id":109836,"name":"Hiram Clawson","orcid":"0000-0002-0480-0545","position":99,"is_corresponding":false},{"id":21320,"name":"Arang Rhie","orcid":"0000-0002-9809-8127","position":0,"is_corresponding":true}],"reference_count":105,"raw_metadata":null,"created_at":"2026-07-18T23:41:52.374756Z","pmid":"33911273","pmcid":"PMC8081667","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":72.2222,"fair_a":75.0,"fair_i":40.0,"fair_r":41.6667,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":72.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"PRJNA489243","grounded":true,"rationale":"The accession PRJNA489243 is a BioProject identifier, which is a persistent identifier scheme accepted at 'yes'.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All raw data, intermediate and final assemblies are publicly available via GenomeArk (https://vgp.github.io/genomeark), archived on NCBI/EBI BioProject under accession PRJNA489243","grounded":true,"rationale":"GenomeArk and NCBI/EBI BioProject are named repositories, both of which are proper nouns listed in the class-1 repository list.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All raw data, intermediate and final assemblies are publicly available via GenomeArk (https://vgp.github.io/genomeark), archived on NCBI/EBI BioProject under accession PRJNA489243 with annotations, and browsable on the UCSC Genome Browser (https://hgdownload.soe.ucsc.edu/hubs/VGP/).","grounded":false,"rationale":"The DAS points to a repository record (GenomeArk and NCBI BioProject) with an accession number, satisfying Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All raw data, intermediate and final assemblies are publicly available","grounded":true,"rationale":"The dataset content is described in a single sentence in running prose, not an itemised inventory. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"archived on NCBI/EBI BioProject under accession PRJNA489243","grounded":true,"rationale":"The dataset identifier (PRJNA489243) appears only in the body text (data availability section), not in the reference list.","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":75.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All raw data, intermediate and final assemblies are publicly available via GenomeArk (https://vgp.github.io/genomeark), archived on NCBI/EBI BioProject under accession PRJNA489243 with annotations","grounded":true,"rationale":"The text gives a route to the data at GenomeArk and NCBI BioProject with no stated precondition; the data are 'publicly available'. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"publicly available","grounded":true,"rationale":"The data availability statement explicitly labels the data as 'publicly available', which is a natural-language synonym for 'open access'. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are genome assemblies from non-human species and are openly available; no gatekeeper is mentioned because no access control is needed.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper states the data are publicly available but does not specify a retention period or persistence commitment. [majority verdict 'no' (3/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file-format token (e.g., FASTA, FASTQ, VCF) is named for the released data; the text only refers to 'assemblies' generically.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"BUSCO vertebrate gene set","grounded":true,"rationale":"The paper names a community standard (BUSCO) applied to the data. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"GRCh38","grounded":false,"rationale":"The paper gives the human reference genome assembly identifier GRCh38, which is an identifier for a resource other than the study's own data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper states a Creative Commons Attribution 4.0 license for the article, but no license is explicitly applied to the data themselves.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"PacBio continuous long reads (CLR) or Oxford Nanopore long reads","grounded":false,"rationale":"The text names specific sequencing technologies (PacBio CLR, Oxford Nanopore) used to produce the data, which are proper-noun instruments. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Extended Data Table 1","grounded":true,"rationale":"Variable definitions are provided in an article table, not in a separate documentation object shipped with the data. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is given for the data; the assemblies are referred to by accession (PRJNA489243) but without a version or release date. [majority verdict 'no' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"https://github.com/VGP/vgp-assembly","grounded":true,"rationale":"The study's code is given a machine-resolvable locator (GitHub URL), which is an authoritative versioned locator.","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"WT207492","grounded":true,"rationale":"The paper gives a Wellcome Trust grant number (WT207492) in the acknowledgements, which is an alphanumeric award identifier.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper states a Creative Commons Attribution 4.0 license for the article, but no license is explicitly applied to the data themselves.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file-format token (e.g., FASTA, FASTQ, VCF) is named for the released data; the text only refers to 'assemblies' generically.","gain":8.33,"priority":"important","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"archived on NCBI/EBI BioProject under accession PRJNA489243","why":"The dataset identifier (PRJNA489243) appears only in the body text (data availability section), not in the reference list.","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is given for the data; the assemblies are referred to by accession (PRJNA489243) but without a version or release date. [majority verdict 'no' (4/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All raw data, intermediate and final assemblies are publicly available via GenomeArk (https://vgp.github.io/genomeark), archived on NCBI/EBI BioProject under accession PRJNA489243 with annotations, and browsable on the UCSC Genome Browser (https://hgdownload.soe.ucsc.edu/hubs/VGP/).","why":"The DAS points to a repository record (GenomeArk and NCBI BioProject) with an accession number, satisfying Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All raw data, intermediate and final assemblies are publicly available","why":"The dataset content is described in a single sentence in running prose, not an itemised inventory. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"PacBio continuous long reads (CLR) or Oxford Nanopore long reads","why":"The text names specific sequencing technologies (PacBio CLR, Oxford Nanopore) used to produce the data, which are proper-noun instruments. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Extended Data Table 1","why":"Variable definitions are provided in an article table, not in a separate documentation object shipped with the data. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are genome assemblies from non-human species and are openly available; no gatekeeper is mentioned because no access control is needed.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"GRCh38","why":"The paper gives the human reference genome assembly identifier GRCh38, which is an identifier for a resource other than the study's own data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper states the data are publicly available but does not specify a retention period or persistence commitment. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:44:42.212612Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}