{"doi":"10.1101/2021.10.15.464561","title":"Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>Ambitious initiatives to coordinate genome sequencing of Earth’s biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.</jats:p>","journal":null,"year":null,"id":637951,"datarank":0.24141568686511508,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.0,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.0,"corpus_percentile":38.6,"corpus_rank":8158,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":3397,"name":"Robert M. Waterhouse","orcid":"0000-0003-4199-9052","position":1,"is_corresponding":false},{"id":237363,"name":"Romain Feron","orcid":"0000-0001-5893-6184","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>Ambitious initiatives to coordinate genome sequencing of Earth’s biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.</jats:p>","is_dataset_classified":null,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19767382","pmcid":null,"openalex_id":"https://openalex.org/W3206437677","authors":[],"funders":[{"funder_name":"Swiss National Science Foundation","grant_id":"202669","title":"Genomic innovations underlying arthropod success and diversity"},{"funder_name":"Swiss National Science Foundation","grant_id":"170664","title":"Exploiting evolutionary signatures to build an enhanced understanding of gene function"}],"total_grants":2,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2022,"count":2},{"year":2023,"count":1},{"year":2024,"count":1}],"oa_status":"green","license":"cc-by","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2021/10/16/2021.10.15.464561.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2021/10/16/2021.10.15.464561.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2021.10.15.464561","host_type":"publisher"},{"url":"https://doi.org/10.1101/2021.10.15.464561","host_type":"repository"},{"url":"https://serval.unil.ch/resource/serval:BIB_1A9AE144B7E8.P001/REF.pdf","host_type":""},{"url":"https://doi.org/10.1093/gigascience/giac006","host_type":""},{"url":"https://academic.oup.com/gigascience/article-pdf/doi/10.1093/gigascience/giac006/42616494/giac006.pdf","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/35217859","host_type":""},{"url":"http://dx.doi.org/10.1093/gigascience/giac006","host_type":""},{"url":"https://dx.doi.org/10.1101/2021.10.15.464561","host_type":""},{"url":"http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_1A9AE144B7E85","host_type":""},{"url":"https://serval.unil.ch/notice/serval:BIB_1A9AE144B7E8","host_type":""}],"fields_of_study":["Genomics and Phylogenetic Studies","Genetic diversity and population structure","Insect symbiosis and bacterial influences","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Workflow","Genome","Data science","Resource (disambiguation)","Benchmarking","Data quality","Quality (philosophy)","Sequence assembly","Reference genome","Biology","Computational biology","Computer science","Geography","Service (business)","Genetics","Gene","Database","Business","Base Sequence","Base Sequence; Chromosome Mapping; Ecosystem; Genome; Genomics/methods; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; BUSCO assessments; arthropod genomes; biodiversity genomics; genome assembly; genome quality database; reproducible workflow","Chromosome Mapping","High-Throughput Nucleotide Sequencing","Genomics","Sequence Analysis, DNA","Technical Note","Ecosystem"],"sdg_mappings":[{"sdg_number":2,"sdg_label":"2. Zero hunger"},{"sdg_number":14,"sdg_label":"14. Life underwater"},{"sdg_number":15,"sdg_label":"15. Life on land"},{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T19:47:44.724038Z","pmid":null,"pmcid":null,"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":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}