{"id":"https://openalex.org/W4376503838","doi":"https://doi.org/10.1093/nar/gkad410","title":"GenomeFLTR: filtering reads made easy","display_name":"GenomeFLTR: filtering reads made easy","publication_year":2023,"publication_date":"2023-05-13","ids":{"openalex":"https://openalex.org/W4376503838","doi":"https://doi.org/10.1093/nar/gkad410","pmid":"https://pubmed.ncbi.nlm.nih.gov/37177997"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkad410","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad410","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad410/50310151/gkad410.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad410/50310151/gkad410.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063512895","display_name":"Edo Dotan","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Edo Dotan","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030937789","display_name":"Michael Alburquerque","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Michael Alburquerque","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040966609","display_name":"Elya Wygoda","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Elya Wygoda","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073566021","display_name":"Doroth\u00e9e Huchon","orcid":"https://orcid.org/0000-0002-5047-244X"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Doroth\u00e9e Huchon","raw_affiliation_strings":["School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":"https://orcid.org/0000-0002-5047-244X","affiliations":[{"raw_affiliation_string":"School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070736617","display_name":"Tal Pupko","orcid":"https://orcid.org/0000-0001-9463-2575"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Tal Pupko","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":"https://orcid.org/0000-0001-9463-2575","affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073566021"],"corresponding_institution_ids":["https://openalex.org/I16391192"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.8073,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.72725341,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"51","issue":"W1","first_page":"W232","last_page":"W236"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.9991999864578247,"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":0.9952999949455261,"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/biology","display_name":"Biology","score":0.6951234340667725},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.47474175691604614},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44601866602897644},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.44422969222068787},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.4409034252166748},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.43831321597099304},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.42710080742836},{"id":"https://openalex.org/keywords/bloom-filter","display_name":"Bloom filter","score":0.42666590213775635},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4258684813976288},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.42293331027030945},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4125812351703644},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.20878827571868896},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.18451282382011414},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16934067010879517},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13651829957962036},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08554863929748535}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6951234340667725},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.47474175691604614},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44601866602897644},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.44422969222068787},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.4409034252166748},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.43831321597099304},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.42710080742836},{"id":"https://openalex.org/C147224247","wikidata":"https://www.wikidata.org/wiki/Q885373","display_name":"Bloom filter","level":2,"score":0.42666590213775635},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4258684813976288},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.42293331027030945},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4125812351703644},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.20878827571868896},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.18451282382011414},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16934067010879517},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13651829957962036},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08554863929748535},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","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":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkad410","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad410","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad410/50310151/gkad410.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:37177997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37177997","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10320065","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10320065","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10320065/pdf/gkad410.pdf","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkad410","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad410","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad410/50310151/gkad410.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2883622317","display_name":null,"funder_award_id":"2818/21","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"},{"id":"https://openalex.org/G7917760792","display_name":null,"funder_award_id":"652/20","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320322596","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4376503838.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W756850952","https://openalex.org/W1976369775","https://openalex.org/W1990086512","https://openalex.org/W2003347102","https://openalex.org/W2017952818","https://openalex.org/W2062163923","https://openalex.org/W2111414304","https://openalex.org/W2112364185","https://openalex.org/W2114392707","https://openalex.org/W2116895571","https://openalex.org/W2121180999","https://openalex.org/W2169123200","https://openalex.org/W2176109601","https://openalex.org/W2253153097","https://openalex.org/W2514173769","https://openalex.org/W2769312509","https://openalex.org/W2891341289","https://openalex.org/W2946874419","https://openalex.org/W2949511413","https://openalex.org/W2952463830","https://openalex.org/W2990618091","https://openalex.org/W2995336106","https://openalex.org/W3010833257","https://openalex.org/W3028050938","https://openalex.org/W3168040031","https://openalex.org/W4213316818","https://openalex.org/W4224035735","https://openalex.org/W4256333965","https://openalex.org/W6651260776","https://openalex.org/W6809885388"],"related_works":["https://openalex.org/W2086572746","https://openalex.org/W2604468458","https://openalex.org/W2157216338","https://openalex.org/W1662107788","https://openalex.org/W121740227","https://openalex.org/W2135966669","https://openalex.org/W2732769800","https://openalex.org/W3082379938","https://openalex.org/W2924589531","https://openalex.org/W2953380184"],"abstract_inverted_index":{"In":[0],"the":[1,26,88,98,101,114,119,122],"last":[2],"decade,":[3],"advances":[4],"in":[5,14,36,81],"sequencing":[6,37],"technology":[7],"have":[8,20],"led":[9],"to":[10,58,73,103,112],"an":[11],"exponential":[12],"increase":[13],"genomic":[15],"data.":[16],"These":[17],"new":[18,55],"data":[19],"dramatically":[21],"changed":[22],"our":[23],"understanding":[24],"of":[25,30,87,94,118,124],"evolution":[27],"and":[28,32,116],"function":[29],"genes":[31],"genomes.":[33],"Despite":[34],"improvements":[35],"technologies,":[38],"identifying":[39],"contaminated":[40,60],"reads":[41],"remains":[42],"a":[43,54,108,125],"complex":[44],"task":[45],"for":[46],"many":[47],"research":[48],"groups.":[49],"Here,":[50],"we":[51],"introduce":[52],"GenomeFLTR,":[53],"web":[56],"server":[57],"filter":[59],"reads.":[61],"Reads":[62],"are":[63],"compared":[64],"against":[65,97],"existing":[66],"sequence":[67],"databases":[68],"from":[69],"various":[70],"representative":[71],"organisms":[72],"detect":[74],"potential":[75],"contaminants.":[76],"The":[77],"main":[78],"features":[79],"implemented":[80],"GenomeFLTR":[82],"are:":[83],"(i)":[84],"automated":[85],"updating":[86],"relevant":[89],"databases;":[90,106],"(ii)":[91],"fast":[92],"comparison":[93],"each":[95],"read":[96],"database;":[99],"(iii)":[100],"ability":[102],"create":[104],"user-specified":[105],"(iv)":[107],"user-friendly":[109],"interactive":[110],"dashboard":[111],"investigate":[113],"origin":[115],"frequency":[117],"contaminations;":[120],"(v)":[121],"generation":[123],"contamination-free":[126],"file.":[127],"Availability:":[128],"https://genomefltr.tau.ac.il/.":[129]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
