{"doi":"10.1105/tpc.17.00514","title":"Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping","abstract":null,"journal":"The Plant Cell","year":2018,"id":591982,"datarank":1.6852829428166283,"base_score":3.7612001156935624,"endowment":3.7612001156935624,"self_citation_contribution":0.5641800173540344,"citation_network_contribution":1.121102925462594,"self_endowment_contribution":0.5641800173540344,"citer_contribution":1.121102925462594,"corpus_percentile":null,"corpus_rank":null,"citation_count":42,"citer_count":37,"citers_with_citation_signal":32,"citers_with_endowment":32,"datacite_reuse_total":0,"is_dataset":false,"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":615111,"name":"R. Kelly Dawe","orcid":"0000-0003-3407-4553","position":1,"is_corresponding":false},{"id":1514724,"name":"Joshua A. Udall","orcid":"0000-0003-0978-4764","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping","abstract":"Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes would be sequenced by two different methods so that one assembly serves as confirmation of the other; however, cost constraints make this approach unlikely. Overreliance on synteny as a means of confirming and ordering contigs will lead to compounded errors. Optical mapping is an accessible and relatively mature technology that can be used for genome assembly validation. We discuss how optical mapping can be used as a validation tool for genome assemblies and how to interpret the results. In addition, we discuss methods for using optical map data to enhance genome assemblies derived from both traditional sequence contigs and Hi-C pseudomolecules.","is_dataset_classified":null,"base_score":3.7612001156935624,"endowment":3.7612001156935624,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"29263086","pmcid":null,"openalex_id":"https://openalex.org/W2779945812","authors":[],"funders":[{"funder_name":"National Science Foundation","grant_id":"1339412","title":"Structural Variation of Diploid and Polyploid Plant Genomes"},{"funder_name":"National Science Foundation","grant_id":"1444514","title":"Functional Genomics of Maize Centromeres"}],"total_grants":2,"fwci":2.4325,"citation_percentile":0.90048516,"influential_citations":0,"citation_trend":[{"year":2018,"count":9},{"year":2019,"count":7},{"year":2020,"count":8},{"year":2021,"count":4},{"year":2022,"count":7},{"year":2023,"count":4},{"year":2025,"count":1},{"year":2026,"count":2}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"http://www.plantcell.org/content/plantcell/30/1/7.full.pdf","host_type":"journal"},{"url":"http://www.plantcell.org/content/plantcell/30/1/7.full.pdf","host_type":"publisher"},{"url":"https://syndication.highwire.org/content/doi/10.1105/tpc.17.00514","host_type":"publisher"},{"url":"https://doi.org/10.1105/tpc.17.00514","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/29263086","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5810561","host_type":"repository"},{"url":"https://dx.doi.org/10.1105/tpc.17.00514","host_type":""}],"fields_of_study":["Genomics and Phylogenetic Studies","Chromosomal and Genetic Variations","Phytoplasmas and Hemiptera pathogens","0301 basic medicine","0303 health sciences","03 medical and health sciences","Chromosome Mapping","Genome, Plant","Optogenetics","Reproducibility of Results","Sequence Analysis, DNA"],"mesh_terms":["Chromosome Mapping","Reproducibility of Results","Sequence Analysis, DNA","Genome, Plant","Optogenetics"],"keywords":["Contig","Synteny","Genome","Sequence assembly","Biology","Computational biology","Optical mapping","Hybrid genome assembly","Whole genome sequencing","Sequence (biology)","Computer science","Genetics","Gene","Optogenetics","Chromosome Mapping","Reproducibility of Results","Sequence Analysis, DNA","Genome, Plant"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-26T11:40:28.311971Z","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":[]}