{"id":"https://openalex.org/W2098531465","doi":"https://doi.org/10.1093/bioinformatics/bts723","title":"ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies","display_name":"ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies","publication_year":2013,"publication_date":"2013-01-09","ids":{"openalex":"https://openalex.org/W2098531465","doi":"https://doi.org/10.1093/bioinformatics/bts723","mag":"2098531465","pmid":"https://pubmed.ncbi.nlm.nih.gov/23303509"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/4/435/48899943/bioinformatics_29_4_435.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/4/435/48899943/bioinformatics_29_4_435.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062082518","display_name":"Scott Clark","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott C. Clark","raw_affiliation_strings":["1 Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA, 2Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 4School of Operations Research and Information Engineering, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA, 2Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 4School of Operations Research and Information Engineering, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082270383","display_name":"Rob Egan","orcid":"https://orcid.org/0000-0001-7080-7801"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Egan","raw_affiliation_strings":["1 Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA, 2Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 4School of Operations Research and Information Engineering, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA, 2Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 4School of Operations Research and Information Engineering, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039019367","display_name":"Peter I. Frazier","orcid":"https://orcid.org/0000-0002-3501-3341"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter I. Frazier","raw_affiliation_strings":["1 Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA, 2Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 4School of Operations Research and Information Engineering, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA, 2Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 4School of Operations Research and Information Engineering, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100781872","display_name":"Zhong Wang","orcid":"https://orcid.org/0000-0002-6307-0458"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhong Wang","raw_affiliation_strings":["1 Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA, 2Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 4School of Operations Research and Information Engineering, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA, 2Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and 4School of Operations Research and Information Engineering, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I205783295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5039019367","https://openalex.org/A5100781872"],"corresponding_institution_ids":["https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I205783295"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":10.3179,"has_fulltext":true,"cited_by_count":207,"citation_normalized_percentile":{"value":0.98941284,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"29","issue":"4","first_page":"435","last_page":"443"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9804999828338623,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9804999828338623,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.004900000058114529,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.0020000000949949026,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.8054103255271912},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6228964328765869},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5582836866378784},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5477988719940186},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5442174077033997},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5163161158561707},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4084862172603607},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34946513175964355},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26933708786964417},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15271049737930298}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8054103255271912},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6228964328765869},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5582836866378784},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5477988719940186},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5442174077033997},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5163161158561707},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4084862172603607},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34946513175964355},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26933708786964417},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15271049737930298},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/4/435/48899943/bioinformatics_29_4_435.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23303509","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23303509","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.719.8848","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.719.8848","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://people.orie.cornell.edu/pfrazier/pub/2013_ClarkEganFrazierWang.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/4/435/48899943/bioinformatics_29_4_435.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6399999856948853,"display_name":"Life below water","id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1677143136","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G2503023272","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3944918260","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4879360136","display_name":"A GRADUATE FELLOWSHIP PROGRAM IN COMPUTATIONAL SCIENCE AND RELATED SCIENCES","funder_award_id":"FG02-97ER25308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5076365615","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G5296923526","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G5602503670","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G5614806141","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G5802748842","display_name":null,"funder_award_id":"DE-AC02-05CH112","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6429026066","display_name":null,"funder_award_id":"DE-AC02-05CH112","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G696937148","display_name":null,"funder_award_id":"DE-FG02-97ER25308","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G7039840861","display_name":null,"funder_award_id":"DE-FG02-97ER25308","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7186324567","display_name":null,"funder_award_id":"DE-FG02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7205239661","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G7672463193","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G805243471","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8684078510","display_name":null,"funder_award_id":"DE-FG02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320317220","display_name":"National Energy Research Scientific Computing Center","ror":"https://ror.org/05v3mvq14"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098531465.pdf","grobid_xml":"https://content.openalex.org/works/W2098531465.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1966711026","https://openalex.org/W1969346416","https://openalex.org/W1979006961","https://openalex.org/W1986245405","https://openalex.org/W1996506104","https://openalex.org/W2012986985","https://openalex.org/W2013381495","https://openalex.org/W2016577330","https://openalex.org/W2023829651","https://openalex.org/W2033083661","https://openalex.org/W2044539313","https://openalex.org/W2044540291","https://openalex.org/W2047927409","https://openalex.org/W2073163969","https://openalex.org/W2081676964","https://openalex.org/W2091232725","https://openalex.org/W2093931624","https://openalex.org/W2108234281","https://openalex.org/W2114133992","https://openalex.org/W2114765236","https://openalex.org/W2118268786","https://openalex.org/W2118526609","https://openalex.org/W2124572097","https://openalex.org/W2124985265","https://openalex.org/W2125826054","https://openalex.org/W2127768708","https://openalex.org/W2128016314","https://openalex.org/W2129220104","https://openalex.org/W2129687578","https://openalex.org/W2132341951","https://openalex.org/W2135361281","https://openalex.org/W2135947999","https://openalex.org/W2152710395","https://openalex.org/W2154503441","https://openalex.org/W2160444236","https://openalex.org/W2161454753","https://openalex.org/W2161546116","https://openalex.org/W2912500497"],"related_works":["https://openalex.org/W2055448750","https://openalex.org/W3134563641","https://openalex.org/W3157741229","https://openalex.org/W1834562783","https://openalex.org/W3098103638","https://openalex.org/W1986608492","https://openalex.org/W2921363728","https://openalex.org/W2279684808","https://openalex.org/W4210830088","https://openalex.org/W2767590279"],"abstract_inverted_index":{"MOTIVATION:":[0],"Researchers":[1],"need":[2,32],"general":[3],"purpose":[4],"methods":[5,26],"for":[6,17],"objectively":[7],"evaluating":[8,77],"the":[9,42,78,138,150,165,217,245,257],"accuracy":[10,79],"of":[11,41,45,80,174,198,228],"single":[12,121,177,229],"and":[13,16,52,95,102,112,122,131,224,231,267],"metagenome":[14,58,232],"assemblies":[15,133],"automatically":[18],"detecting":[19],"any":[20],"errors":[21,118,201],"they":[22,34],"may":[23],"contain.":[24],"Current":[25],"do":[27],"not":[28],"fully":[29],"meet":[30],"this":[31,62],"because":[33],"require":[35],"a":[36,84,181,185,203,221],"reference,":[37],"only":[38],"consider":[39],"one":[40],"many":[43],"aspects":[44],"assembly":[46,82,233,246],"quality":[47],"or":[48,242],"lack":[49],"statistical":[50,89],"justification,":[51],"none":[53],"are":[54],"designed":[55],"to":[56,239,243],"evaluate":[57],"assemblies.":[59],"RESULTS:":[60],"In":[61,215],"article,":[63],"we":[64],"present":[65],"an":[66,81],"Assembly":[67],"Likelihood":[68],"Evaluation":[69],"(ALE)":[70],"framework":[71,92,219],"that":[72],"overcomes":[73],"these":[74],"limitations,":[75],"systematically":[76],"in":[83,119,135,180,202,265],"reference-independent":[85,223],"manner":[86],"using":[87],"rigorous":[88,226],"methods.":[90],"This":[91],"is":[93,250,263],"comprehensive,":[94,222],"integrates":[96],"read":[97,110],"quality,":[98],"mate":[99],"pair":[100],"orientation":[101],"insert":[103],"length":[104],"(for":[105],"paired-end":[106],"reads),":[107],"sequencing":[108],"coverage,":[109],"alignment":[111],"k-mer":[113],"frequency.":[114],"ALE":[115,144,171,195,218,249],"pinpoints":[116],"synthetic":[117,200],"both":[120],"metagenomic":[123],"assemblies,":[124],"including":[125],"single-base":[126,166],"errors,":[127],"insertions/deletions,":[128],"genome":[129,139,230],"rearrangements":[130],"chimeric":[132],"presented":[134],"metagenomes.":[136],"At":[137,164],"level":[140,167],"with":[141,168],"real-world":[142],"data,":[143,170,194],"identifies":[145,196],"three":[146],"large":[147],"misassemblies":[148,241],"from":[149,184],"Spirochaeta":[151],"smaragdinae":[152],"finished":[153],"genome,":[154,206],"which":[155,235],"were":[156],"all":[157],"independently":[158],"validated":[159],"by":[160],"Pacific":[161,192,209],"Biosciences":[162,193],"sequencing.":[163],"Illumina":[169],"recovers":[172],"215":[173],"222":[175],"(97%)":[176],"nucleotide":[178],"variants":[179],"training":[182],"set":[183],"GC-rich":[186],"Rhodobacter":[187],"sphaeroides":[188],"genome.":[189],"Using":[190],"real":[191],"12":[197,199],"Lambda":[204],"Phage":[205],"surpassing":[207],"even":[208],"Biosciences'":[210],"own":[211],"variant":[212],"caller,":[213],"EviCons.":[214],"summary,":[216],"provides":[220],"statistically":[225],"measure":[227],"accuracy,":[234],"can":[236],"be":[237],"used":[238],"identify":[240],"optimize":[244],"process.":[247],"AVAILABILITY:":[248],"released":[251],"as":[252],"open":[253],"source":[254],"software":[255],"under":[256],"UoI/NCSA":[258],"license":[259],"at":[260],"http://www.alescore.org.":[261],"It":[262],"implemented":[264],"C":[266],"Python.":[268]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":32},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":25},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":15}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-10-10T00:00:00"}
