{"id":"https://openalex.org/W2148515298","doi":"https://doi.org/10.1186/s12859-015-0595-z","title":"BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS","display_name":"BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS","publication_year":2015,"publication_date":"2015-06-30","ids":{"openalex":"https://openalex.org/W2148515298","doi":"https://doi.org/10.1186/s12859-015-0595-z","mag":"2148515298","pmid":"https://pubmed.ncbi.nlm.nih.gov/26130132"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0595-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0595-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0595-z","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/counter/pdf/10.1186/s12859-015-0595-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067077141","display_name":"Bruno Fosso","orcid":"https://orcid.org/0000-0003-2324-086X"},"institutions":[{"id":"https://openalex.org/I4210148743","display_name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies","ror":"https://ror.org/05nzf7q96","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210148743","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Bruno Fosso","raw_affiliation_strings":["Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy. b.fosso@ibbe.cnr.it","Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy. b.fosso@ibbe.cnr.it","institution_ids":["https://openalex.org/I4210148743"]},{"raw_affiliation_string":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy","institution_ids":["https://openalex.org/I4210148743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012981755","display_name":"M\u00f3nica Santamar\u00eda","orcid":"https://orcid.org/0000-0003-1488-6052"},"institutions":[{"id":"https://openalex.org/I4210148743","display_name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies","ror":"https://ror.org/05nzf7q96","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210148743","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Monica Santamaria","raw_affiliation_strings":["Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy. m.santamaria@ibbe.cnr.it","Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy. m.santamaria@ibbe.cnr.it","institution_ids":["https://openalex.org/I4210148743"]},{"raw_affiliation_string":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy","institution_ids":["https://openalex.org/I4210148743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070018825","display_name":"Marinella Marzano","orcid":"https://orcid.org/0000-0002-9996-8817"},"institutions":[{"id":"https://openalex.org/I4210148743","display_name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies","ror":"https://ror.org/05nzf7q96","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210148743","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marinella Marzano","raw_affiliation_strings":["Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy. marzano.marinella@gmail.com","Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy. marzano.marinella@gmail.com","institution_ids":["https://openalex.org/I4210148743"]},{"raw_affiliation_string":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy","institution_ids":["https://openalex.org/I4210148743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107502255","display_name":"Daniel Alonso-Alemany","orcid":null},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Daniel Alonso-Alemany","raw_affiliation_strings":["Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain. dalonso@cs.upc.edu","Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain. dalonso@cs.upc.edu","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005629452","display_name":"Gabriel Valiente","orcid":"https://orcid.org/0000-0001-9194-2703"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Gabriel Valiente","raw_affiliation_strings":["Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain. valiente@cs.upc.edu","Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain. valiente@cs.upc.edu","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005416001","display_name":"Giacinto Donvito","orcid":"https://orcid.org/0000-0002-0628-1080"},"institutions":[{"id":"https://openalex.org/I4210112283","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Bari","ror":"https://ror.org/022hq6c49","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210112283"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giacinto Donvito","raw_affiliation_strings":["National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy. giacinto.donvito@ba.infn.it","National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy. giacinto.donvito@ba.infn.it","institution_ids":["https://openalex.org/I4210112283"]},{"raw_affiliation_string":"National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009283925","display_name":"A. Monaco","orcid":"https://orcid.org/0000-0002-5968-8642"},"institutions":[{"id":"https://openalex.org/I4210112283","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Bari","ror":"https://ror.org/022hq6c49","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210112283"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alfonso Monaco","raw_affiliation_strings":["National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy. Alfonso.Monaco@ba.infn.it","National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy. Alfonso.Monaco@ba.infn.it","institution_ids":["https://openalex.org/I4210112283"]},{"raw_affiliation_string":"National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005277471","display_name":"Pasquale Notarangelo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210112283","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Bari","ror":"https://ror.org/022hq6c49","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210112283"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Pasquale Notarangelo","raw_affiliation_strings":["National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy. Pasquale.Notarangelo@ba.infn.it","National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy. Pasquale.Notarangelo@ba.infn.it","institution_ids":["https://openalex.org/I4210112283"]},{"raw_affiliation_string":"National Institute of Nuclear Physics, via E. Orabona 4, Bari, 70125, Italy","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005312066","display_name":"Graziano Pesole","orcid":"https://orcid.org/0000-0003-3663-0859"},"institutions":[{"id":"https://openalex.org/I4210148743","display_name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies","ror":"https://ror.org/05nzf7q96","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210148743","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I5561750","display_name":"University of Bari Aldo Moro","ror":"https://ror.org/027ynra39","country_code":"IT","type":"education","lineage":["https://openalex.org/I5561750"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Graziano Pesole","raw_affiliation_strings":["Center of Excellence in Comparative Genomics, University of Bari \"A. Moro\", via E. Orabona, 4, Bari, 70125, Italy. graziano.pesole@uniba.it","Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari \"A. Moro\", via E. Orabona 4, Bari, 70125, Italy. graziano.pesole@uniba.it","Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy. graziano.pesole@uniba.it","Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari \"A. Moro\", via E. Orabona 4, Bari, 70125, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence in Comparative Genomics, University of Bari \"A. Moro\", via E. Orabona, 4, Bari, 70125, Italy. graziano.pesole@uniba.it","institution_ids":["https://openalex.org/I5561750"]},{"raw_affiliation_string":"Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari \"A. Moro\", via E. Orabona 4, Bari, 70125, Italy. graziano.pesole@uniba.it","institution_ids":["https://openalex.org/I5561750"]},{"raw_affiliation_string":"Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, via Amendola 165/A, Bari, 70126, Italy. graziano.pesole@uniba.it","institution_ids":["https://openalex.org/I4210148743"]},{"raw_affiliation_string":"Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari \"A. Moro\", via E. Orabona 4, Bari, 70125, Italy","institution_ids":["https://openalex.org/I5561750"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5005312066"],"corresponding_institution_ids":["https://openalex.org/I4210148743","https://openalex.org/I5561750"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.3429,"has_fulltext":true,"cited_by_count":57,"citation_normalized_percentile":{"value":0.88975142,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"203","last_page":"203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6348000168800354,"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":0.6348000168800354,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.13850000500679016,"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/T10066","display_name":"Gut microbiota and health","score":0.07930000126361847,"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":0.8639777898788452},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5980052351951599},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5951226353645325},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5907895565032959},{"id":"https://openalex.org/keywords/amplicon","display_name":"Amplicon","score":0.5361179709434509},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.48424312472343445},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.431618332862854},{"id":"https://openalex.org/keywords/environmental-dna","display_name":"Environmental DNA","score":0.4290092885494232},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3839753270149231},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.382129967212677},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35047394037246704},{"id":"https://openalex.org/keywords/biodiversity","display_name":"Biodiversity","score":0.21371334791183472},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.17014819383621216},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1625710427761078},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13585638999938965},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.09283703565597534}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8639777898788452},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5980052351951599},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5951226353645325},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5907895565032959},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.5361179709434509},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48424312472343445},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.431618332862854},{"id":"https://openalex.org/C2779969263","wikidata":"https://www.wikidata.org/wiki/Q25098939","display_name":"Environmental DNA","level":3,"score":0.4290092885494232},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3839753270149231},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.382129967212677},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35047394037246704},{"id":"https://openalex.org/C130217890","wikidata":"https://www.wikidata.org/wiki/Q47041","display_name":"Biodiversity","level":2,"score":0.21371334791183472},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.17014819383621216},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1625710427761078},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13585638999938965},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.09283703565597534},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044822","descriptor_name":"Biodiversity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044822","descriptor_name":"Biodiversity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044822","descriptor_name":"Biodiversity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":6,"locations":[{"id":"doi:10.1186/s12859-015-0595-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0595-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0595-z","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:26130132","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26130132","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:recercat.cat:2072/255063","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/77809","pdf_url":null,"source":{"id":"https://openalex.org/S4306402147","display_name":"RECERCAT (Consorci de Serveis Universitaris de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210090028","host_organization_name":"Consorci de Serveis Universitaris de Catalunya","host_organization_lineage":["https://openalex.org/I4210090028"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:upcommons.upc.edu:2117/77809","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/77809","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:europepmc.org:3453932","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4486701","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:ricerca.uniba.it:11586/166772","is_oa":true,"landing_page_url":"http://hdl.handle.net/11586/166772","pdf_url":null,"source":{"id":"https://openalex.org/S4377196296","display_name":"CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5561750","host_organization_name":"University of Bari Aldo Moro","host_organization_lineage":["https://openalex.org/I5561750"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0595-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0595-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0595-z","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322651","display_name":"Consiglio Nazionale delle Ricerche","ror":"https://ror.org/04zaypm56"},{"id":"https://openalex.org/F4320325020","display_name":"LifeWatch \u2013 Niclas \u00d6berg Foundation","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2148515298.pdf","grobid_xml":"https://content.openalex.org/works/W2148515298.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1583240815","https://openalex.org/W1963744685","https://openalex.org/W1972767119","https://openalex.org/W1983320630","https://openalex.org/W1988925586","https://openalex.org/W1993038297","https://openalex.org/W1995962575","https://openalex.org/W2011546759","https://openalex.org/W2019791882","https://openalex.org/W2055043387","https://openalex.org/W2061177996","https://openalex.org/W2065398612","https://openalex.org/W2066452478","https://openalex.org/W2072970694","https://openalex.org/W2096525273","https://openalex.org/W2100947741","https://openalex.org/W2103296919","https://openalex.org/W2106308757","https://openalex.org/W2107903949","https://openalex.org/W2108718991","https://openalex.org/W2111560651","https://openalex.org/W2115701239","https://openalex.org/W2120895683","https://openalex.org/W2124351063","https://openalex.org/W2136482257","https://openalex.org/W2142678031","https://openalex.org/W2146077306","https://openalex.org/W2153993827","https://openalex.org/W2154449852","https://openalex.org/W2155066423","https://openalex.org/W2157107905","https://openalex.org/W2157539385","https://openalex.org/W2161645441","https://openalex.org/W2170551349","https://openalex.org/W2792840714","https://openalex.org/W4250297812","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4281567513","https://openalex.org/W2945250978","https://openalex.org/W4280653686","https://openalex.org/W2970289413","https://openalex.org/W3216140544","https://openalex.org/W3032384960","https://openalex.org/W3133990339","https://openalex.org/W3034807827","https://openalex.org/W4386105821","https://openalex.org/W3088570659"],"abstract_inverted_index":{"BACKGROUND:":[0],"Substantial":[1],"advances":[2],"in":[3,13,31,72,112,134,167,223,279],"microbiology,":[4],"molecular":[5],"evolution":[6],"and":[7,25,79,157,185,219,269,277,283],"biodiversity":[8],"have":[9],"been":[10],"carried":[11,253],"out":[12,254],"recent":[14],"years":[15],"thanks":[16],"to":[17,21,93,129,159,262],"Metagenomics,":[18],"which":[19],"allows":[20,179],"unveil":[22],"the":[23,36,42,62,73,80,98,109,149,180,191,265],"composition":[24],"functions":[26],"of":[27,65,77,82,102,108,120,137,147,182,281,285],"mixed":[28],"microbial":[29,139],"communities":[30,140],"any":[32],"environmental":[33,138],"niche.":[34],"If":[35],"investigation":[37],"is":[38,55,123,209,220,233],"aimed":[39],"only":[40],"at":[41,217,225],"microbiome":[43],"taxonomic":[44,75,135,161,287],"structure,":[45],"a":[46,66,124,142,212,234,257],"target-based":[47],"metagenomic":[48],"approach,":[49],"here":[50],"also":[51,221],"referred":[52],"as":[53],"Meta-barcoding,":[54],"generally":[56],"applied.":[57],"This":[58],"approach":[59],"commonly":[60],"involves":[61],"selective":[63],"amplification":[64],"species-specific":[67],"genetic":[68],"marker":[69],"(DNA":[70],"meta-barcode)":[71],"whole":[74],"range":[76],"interest":[78],"exploration":[81],"its":[83,175],"taxon-related":[84],"variants":[85],"through":[86],"High-Throughput":[87],"Sequencing":[88],"(HTS)":[89],"technologies.":[90],"The":[91],"accessibility":[92],"proper":[94],"computational":[95],"systems":[96],"for":[97,228,237,244],"large-scale":[99],"bioinformatic":[100,126],"analysis":[101,119,181,241],"HTS":[103,201,239],"data":[104,155,194,240],"represents,":[105],"currently,":[106],"one":[107],"major":[110],"challenges":[111],"advanced":[113],"Meta-barcoding":[114,171,238],"projects.":[115],"RESULTS:":[116],"BioMaS":[117,178,208,232,274],"(Bioinformatic":[118],"Metagenomic":[121],"AmpliconS)":[122],"new":[125],"pipeline":[127,236],"designed":[128,170,243,261],"support":[130],"biomolecular":[131],"researchers":[132],"involved":[133],"studies":[136],"by":[141,255],"completely":[143],"automated":[144],"workflow,":[145],"comprehensive":[146],"all":[148],"fundamental":[150],"steps,":[151],"from":[152,190,195],"raw":[153,192],"sequence":[154,288],"upload":[156],"cleaning":[158],"final":[160],"identification,":[162],"that":[163,273],"are":[164],"absolutely":[165],"required":[166],"an":[168],"appropriately":[169],"HTS-based":[172],"experiment.":[173],"In":[174],"current":[176],"version,":[177],"both":[183],"bacterial":[184,268],"fungal":[186,270],"environments":[187],"starting":[188],"directly":[189],"sequencing":[193],"either":[196],"Roche":[197],"454":[198],"or":[199],"Illumina":[200,229],"platforms,":[202],"following":[203],"two":[204],"alternative":[205],"paths,":[206],"respectively.":[207],"implemented":[210],"into":[211],"public":[213],"web":[214],"service":[215],"available":[216,222],"https://recasgateway.ba.infn.it/":[218],"Galaxy":[224],"http://galaxy.cloud.ba.infn.it:8080":[226],"(only":[227],"data).":[230],"CONCLUSION:":[231],"friendly":[235],"specifically":[242],"users":[245],"without":[246],"particular":[247],"computing":[248],"skills.":[249],"A":[250],"comparative":[251],"benchmark,":[252],"using":[256],"simulated":[258],"dataset":[259],"suitably":[260],"broadly":[263],"represent":[264],"currently":[266],"known":[267],"world,":[271],"showed":[272],"outperforms":[275],"QIIME":[276],"MOTHUR":[278],"terms":[280],"extent":[282],"accuracy":[284],"deep":[286],"assignments.":[289]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
