{"id":"https://openalex.org/W2591953849","doi":"https://doi.org/10.5220/0006150500590067","title":"SKraken: Fast and Sensitive Classification of Short Metagenomic Reads based on Filtering Uninformative k-mers","display_name":"SKraken: Fast and Sensitive Classification of Short Metagenomic Reads based on Filtering Uninformative k-mers","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2591953849","doi":"https://doi.org/10.5220/0006150500590067","mag":"2591953849"},"language":"en","primary_location":{"id":"doi:10.5220/0006150500590067","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0006150500590067","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.5220/0006150500590067","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069081225","display_name":"Davide Marchiori","orcid":"https://orcid.org/0000-0001-7914-5568"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Davide Marchiori","raw_affiliation_strings":["University of Padova, Italy"],"affiliations":[{"raw_affiliation_string":"University of Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067815810","display_name":"Matteo Comin","orcid":"https://orcid.org/0000-0001-8545-4359"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Matteo Comin","raw_affiliation_strings":["University of Padova, Italy"],"affiliations":[{"raw_affiliation_string":"University of Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5069081225"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":null,"apc_paid":null,"fwci":0.7443,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.68889257,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"59","last_page":"67"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9894999861717224,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9894999861717224,"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/T10885","display_name":"Gene expression and cancer classification","score":0.961899995803833,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9315999746322632,"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":0.8355161547660828},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6718472242355347},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3658639192581177},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3378053307533264},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33102643489837646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18509110808372498},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08027926087379456},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07043242454528809}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8355161547660828},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6718472242355347},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3658639192581177},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3378053307533264},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33102643489837646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18509110808372498},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08027926087379456},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07043242454528809}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5220/0006150500590067","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0006150500590067","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"},{"id":"pmh:oai:www.research.unipd.it:11577/3227449","is_oa":false,"landing_page_url":"http://hdl.handle.net/11577/3227449","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"doi:10.5220/0006150500590067","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0006150500590067","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2210738511","https://openalex.org/W2474302342","https://openalex.org/W1910109602","https://openalex.org/W4297131566","https://openalex.org/W2017364432","https://openalex.org/W2080583581","https://openalex.org/W3158976456","https://openalex.org/W2767445485","https://openalex.org/W4285082713","https://openalex.org/W2102118387"],"abstract_inverted_index":{"The":[0,18,129],"study":[1],"of":[2,59,89,110,151],"microbial":[3],"communities":[4],"is":[5,10,26,97,114],"an":[6,78],"emerging":[7],"field":[8],"that":[9,140],"revolutionizing":[11],"many":[12],"disciplines":[13],"from":[14],"ecology":[15],"to":[16,27,34,81,116],"medicine.":[17],"major":[19],"problem":[20],"when":[21],"analyzing":[22],"a":[23,87,108],"metagenomic":[24,84],"sample":[25,40],"taxonomic":[28,105],"annotate":[29],"its":[30],"reads":[31,85],"in":[32,38,50,57,143,149],"order":[33],"identify":[35],"the":[36,39,51,55,93,104,118,146],"species":[37],"and":[41,61,135,153],"their":[42],"relative":[43],"abundance.":[44],"Many":[45],"tools":[46],"have":[47],"been":[48],"developed":[49],"recent":[52],"years,":[53],"however":[54],"performance":[56,131],"terms":[58,150],"precision":[60,152],"speed":[62],"are":[63],"not":[64],"always":[65],"adequate":[66],"for":[67,122],"these":[68],"very":[69],"large":[70],"datasets.":[71],"In":[72],"this":[73],"work":[74],"we":[75],"present":[76],"SKraken":[77,96,113,141],"efficient":[79],"approach":[80],"accurately":[82],"classify":[83],"against":[86],"set":[88,109],"reference":[90],"genomes,":[91],"e.g.":[92],"NCBI/RefSeq":[94],"database.":[95],"based":[98],"on":[99,132],"k-mers":[100,121],"statistics":[101],"combined":[102],"with":[103],"tree.":[106],"Given":[107],"target":[111],"genomes":[112],"able":[115],"detect":[117],"most":[119,144],"representative":[120],"each":[123],"species,":[124],"filtering":[125],"out":[126],"uninformative":[127],"k-mers.":[128],"classification":[130],"several":[133],"synthetic":[134],"real":[136],"metagenomics":[137],"datasets":[138],"shows":[139],"achieves":[142],"cases":[145],"best":[147],"performances":[148],"...":[154]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
