{"id":"https://openalex.org/W3087467602","doi":"https://doi.org/10.1186/s12859-020-03628-w","title":"Metagenomic analysis through the extended Burrows-Wheeler transform","display_name":"Metagenomic analysis through the extended Burrows-Wheeler transform","publication_year":2020,"publication_date":"2020-09-01","ids":{"openalex":"https://openalex.org/W3087467602","doi":"https://doi.org/10.1186/s12859-020-03628-w","mag":"3087467602","pmid":"https://pubmed.ncbi.nlm.nih.gov/32938362"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03628-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03628-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03628-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03628-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091484790","display_name":"Veronica Guerrini","orcid":"https://orcid.org/0000-0001-8888-9243"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Veronica Guerrini","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 di Pisa, Largo B. Pontecorvo, 3, Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 di Pisa, Largo B. Pontecorvo, 3, Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016168980","display_name":"Felipe A. Louza","orcid":"https://orcid.org/0000-0003-2931-1470"},"institutions":[{"id":"https://openalex.org/I80850581","display_name":"Universidade Federal de Uberl\u00e2ndia","ror":"https://ror.org/04x3wvr31","country_code":"BR","type":"education","lineage":["https://openalex.org/I80850581"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Felipe A. Louza","raw_affiliation_strings":["Faculty of Electrical Engineering, Federal University of Uberl\u00e2ndia, Uberl\u00e2ndia, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Electrical Engineering, Federal University of Uberl\u00e2ndia, Uberl\u00e2ndia, Brazil","institution_ids":["https://openalex.org/I80850581"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003859151","display_name":"Giovanna Rosone","orcid":"https://orcid.org/0000-0001-5075-1214"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]},{"id":"https://openalex.org/I4210160382","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Pisa","ror":"https://ror.org/05symbg58","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210160382"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Giovanna Rosone","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 di Pisa, Largo B. Pontecorvo, 3, Pisa, Italy. giovanna.rosone@unipi.it","Dipartimento di Informatica, Universit\u00e0 di Pisa, Largo B. Pontecorvo, 3, Pisa, Italy"],"raw_orcid":"https://orcid.org/0000-0001-5075-1214","affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 di Pisa, Largo B. Pontecorvo, 3, Pisa, Italy. giovanna.rosone@unipi.it","institution_ids":["https://openalex.org/I108290504","https://openalex.org/I4210160382"]},{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 di Pisa, Largo B. Pontecorvo, 3, Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003859151"],"corresponding_institution_ids":["https://openalex.org/I108290504","https://openalex.org/I4210160382"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.8338,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.71795851,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"21","issue":"S8","first_page":"299","last_page":"299"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7833999991416931,"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":0.7833999991416931,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.04899999871850014,"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/T10066","display_name":"Gut microbiota and health","score":0.03830000013113022,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.9599714279174805},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5637544393539429},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.478071928024292},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4644728899002075},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.43181276321411133},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.4108710289001465},{"id":"https://openalex.org/keywords/taxonomic-rank","display_name":"Taxonomic rank","score":0.4108377695083618},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3868650197982788},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3625609278678894},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3584873080253601},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33155184984207153},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.2880167067050934},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09416797757148743}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9599714279174805},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5637544393539429},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.478071928024292},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4644728899002075},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.43181276321411133},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.4108710289001465},{"id":"https://openalex.org/C189592816","wikidata":"https://www.wikidata.org/wiki/Q427626","display_name":"Taxonomic rank","level":3,"score":0.4108377695083618},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3868650197982788},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3625609278678894},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3584873080253601},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33155184984207153},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.2880167067050934},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09416797757148743},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-020-03628-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03628-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03628-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32938362","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32938362","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:arpi.unipi.it:11568/1061184","is_oa":true,"landing_page_url":"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03628-w","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:0a21ed84c0734c7bb82f1a2e1a0601f0","is_oa":true,"landing_page_url":"https://doaj.org/article/0a21ed84c0734c7bb82f1a2e1a0601f0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss S8, Pp 1-25 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7493373","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7493373","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03628-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03628-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03628-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G1343878812","display_name":null,"funder_award_id":"RBSI146R5L","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"}],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3087467602.pdf","grobid_xml":"https://content.openalex.org/works/W3087467602.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1494345838","https://openalex.org/W1495913768","https://openalex.org/W1950227463","https://openalex.org/W1969173824","https://openalex.org/W1978173716","https://openalex.org/W1987760161","https://openalex.org/W1991866789","https://openalex.org/W2003347102","https://openalex.org/W2013226864","https://openalex.org/W2017965217","https://openalex.org/W2025648894","https://openalex.org/W2034214367","https://openalex.org/W2040539953","https://openalex.org/W2043646600","https://openalex.org/W2051158076","https://openalex.org/W2051511420","https://openalex.org/W2055043387","https://openalex.org/W2086782013","https://openalex.org/W2124985265","https://openalex.org/W2131106408","https://openalex.org/W2134283755","https://openalex.org/W2143423077","https://openalex.org/W2150208009","https://openalex.org/W2158322625","https://openalex.org/W2159954944","https://openalex.org/W2165571470","https://openalex.org/W2170725655","https://openalex.org/W2171963266","https://openalex.org/W2182091750","https://openalex.org/W2337747100","https://openalex.org/W2339316959","https://openalex.org/W2415159633","https://openalex.org/W2515836512","https://openalex.org/W2604363154","https://openalex.org/W2620416450","https://openalex.org/W2736821863","https://openalex.org/W2753495445","https://openalex.org/W2758005814","https://openalex.org/W2761430568","https://openalex.org/W2774498188","https://openalex.org/W2809922887","https://openalex.org/W2907815526","https://openalex.org/W2914940273","https://openalex.org/W2920034498","https://openalex.org/W2920807403","https://openalex.org/W2945220023","https://openalex.org/W2947183814","https://openalex.org/W2949351818","https://openalex.org/W2951160681","https://openalex.org/W2951176108","https://openalex.org/W2952152744","https://openalex.org/W2952859099","https://openalex.org/W2962729511","https://openalex.org/W2963963068","https://openalex.org/W2963995493","https://openalex.org/W2964007100","https://openalex.org/W2968450569","https://openalex.org/W2990618091","https://openalex.org/W3103359476","https://openalex.org/W3105789150","https://openalex.org/W4230945265","https://openalex.org/W6685669702"],"related_works":["https://openalex.org/W1222064643","https://openalex.org/W1543301402","https://openalex.org/W1604004112","https://openalex.org/W3023731925","https://openalex.org/W2786547608","https://openalex.org/W4283818647","https://openalex.org/W8235432","https://openalex.org/W2950883119","https://openalex.org/W4385414771","https://openalex.org/W200507450"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,56,179,228],"development":[2],"of":[3,16,30,38,58,71,82,110,140,146,150,153,172,198,250,257,268,271,302,310],"Next":[4],"Generation":[5],"Sequencing":[6],"(NGS)":[7],"has":[8],"had":[9],"a":[10,49,79,119,138,220,282],"major":[11],"impact":[12],"on":[13,205,219,231],"the":[14,24,31,35,43,54,68,93,108,135,147,154,161,196,224,232,241,258,266,272,286,305,308],"study":[15],"genetic":[17],"sequences.":[18],"Among":[19],"problems":[20],"that":[21,45,129,166,236,291,301],"researchers":[22],"in":[23,48,78,88,100,134,215,318],"field":[25],"have":[26],"to":[27,65,137,194,295,300],"face,":[28],"one":[29],"most":[32],"challenging":[33],"is":[34,76,186,238,275,293],"taxonomic":[36,244],"classification":[37,128,297],"metagenomic":[39,86,127],"reads,":[40],"i.e.,":[41],"identifying":[42],"microorganisms":[44],"are":[46,62,262],"present":[47],"sample":[50,136],"collected":[51],"directly":[52],"from":[53,208,223],"environment.":[55],"analysis":[57,217],"environmental":[59,111],"samples":[60],"(metagenomes)":[61],"particularly":[63],"important":[64],"figure":[66],"out":[67],"microbial":[69],"composition":[70],"different":[72],"ecosystems":[73],"and":[74,97,123,157,218,252,265,313],"it":[75],"used":[77,243],"wide":[80],"variety":[81],"fields:":[83],"for":[84,126],"instance,":[85],"studies":[87],"agriculture":[89],"can":[90,103,168],"help":[91],"understanding":[92],"interactions":[94],"between":[95],"plants":[96],"microbes,":[98],"or":[99],"ecology,":[101],"they":[102],"provide":[104],"valuable":[105],"insights":[106],"into":[107],"functions":[109],"communities.":[112],"RESULTS:":[113],"In":[114,192],"this":[115],"paper,":[116],"we":[117,158,167,201,289],"describe":[118],"new":[120],"lightweight":[121],"alignment-free":[122],"assembly-free":[124],"framework":[125],"compares":[130],"each":[131],"unknown":[132,170],"sequence":[133],"collection":[139],"known":[141],"genomes.":[142],"We":[143],"take":[144],"advantage":[145],"combinatorial":[148],"properties":[149],"an":[151],"extension":[152],"Burrows-Wheeler":[155],"transform,":[156],"sequentially":[159],"scan":[160],"required":[162],"data":[163,207,234],"structures,":[164],"so":[165],"analyze":[169],"sequences":[171],"large":[173],"collections":[174],"using":[175],"little":[176],"internal":[177],"memory.":[178],"tool":[180],"LiME":[181,237,292],"(Lightweight":[182],"Metagenomics":[183],"via":[184],"eBWT)":[185],"available":[187],"at":[188],"https://github.com/veronicaguerrini/LiME":[189],".":[190],"CONCLUSIONS:":[191],"order":[193],"assess":[195],"reliability":[197],"our":[199,311],"approach,":[200],"run":[202],"several":[203],"experiments":[204,306],"NGS":[206],"two":[209],"simulated":[210,233],"metagenomes":[211],"among":[212],"those":[213],"provided":[214],"benchmarking":[216],"real":[221,287],"metagenome":[222],"Human":[225],"Microbiome":[226],"Project.":[227],"experiment":[229],"results":[230,298],"show":[235,290],"competitive":[239],"with":[240],"widely":[242],"classifiers.":[245],"It":[246],"achieves":[247],"high":[248,283,315],"levels":[249],"precision":[251],"specificity":[253],"-":[254,279],"e.g.":[255],"99.9%":[256],"positive":[259],"control":[260,274,320],"reads":[261,270],"correctly":[263],"assigned":[264],"percentage":[267],"classified":[269],"negative":[273,319],"less":[276],"than":[277],"0.01%":[278],"while":[280],"keeping":[281],"sensitivity.":[284],"On":[285],"metagenome,":[288],"able":[294],"deliver":[296],"comparable":[299],"MagicBlast.":[303],"Overall,":[304],"confirm":[307],"effectiveness":[309],"method":[312],"its":[314],"accuracy":[316],"even":[317],"samples.":[321]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
