{"id":"https://openalex.org/W2597444305","doi":"https://doi.org/10.1186/s13015-017-0097-9","title":"Gerbil: a fast and memory-efficient\u00a0k-mer counter with GPU-support","display_name":"Gerbil: a fast and memory-efficient\u00a0k-mer counter with GPU-support","publication_year":2017,"publication_date":"2017-03-31","ids":{"openalex":"https://openalex.org/W2597444305","doi":"https://doi.org/10.1186/s13015-017-0097-9","mag":"2597444305","pmid":"https://pubmed.ncbi.nlm.nih.gov/28373894"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-017-0097-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0097-9","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0097-9","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0097-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022032918","display_name":"Marius Erbert","orcid":null},"institutions":[{"id":"https://openalex.org/I68956291","display_name":"Martin Luther University Halle-Wittenberg","ror":"https://ror.org/05gqaka33","country_code":"DE","type":"education","lineage":["https://openalex.org/I68956291"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Marius Erbert","raw_affiliation_strings":["Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saae), Germany","Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saae), Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saae), Germany","institution_ids":["https://openalex.org/I68956291"]},{"raw_affiliation_string":"Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saae), Germany","institution_ids":["https://openalex.org/I68956291"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074217174","display_name":"Steffen Rechner","orcid":"https://orcid.org/0000-0003-3445-8645"},"institutions":[{"id":"https://openalex.org/I68956291","display_name":"Martin Luther University Halle-Wittenberg","ror":"https://ror.org/05gqaka33","country_code":"DE","type":"education","lineage":["https://openalex.org/I68956291"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Steffen Rechner","raw_affiliation_strings":["Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saae), Germany","Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saae), Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saae), Germany","institution_ids":["https://openalex.org/I68956291"]},{"raw_affiliation_string":"Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saae), Germany","institution_ids":["https://openalex.org/I68956291"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006211424","display_name":"Matthias M\u00fcller\u2010Hannemann","orcid":"https://orcid.org/0000-0001-6976-0006"},"institutions":[{"id":"https://openalex.org/I68956291","display_name":"Martin Luther University Halle-Wittenberg","ror":"https://ror.org/05gqaka33","country_code":"DE","type":"education","lineage":["https://openalex.org/I68956291"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias M\u00fcller-Hannemann","raw_affiliation_strings":["Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saae), Germany","Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saae), Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saae), Germany","institution_ids":["https://openalex.org/I68956291"]},{"raw_affiliation_string":"Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saae), Germany","institution_ids":["https://openalex.org/I68956291"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5022032918"],"corresponding_institution_ids":["https://openalex.org/I68956291"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":6.7875,"has_fulltext":true,"cited_by_count":81,"citation_normalized_percentile":{"value":0.97114972,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"12","issue":"1","first_page":"9","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11478","display_name":"Caching and Content Delivery","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9940000176429749,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6978647708892822},{"id":"https://openalex.org/keywords/gerbil","display_name":"Gerbil","score":0.5027832984924316},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3290413022041321},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10018482804298401}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6978647708892822},{"id":"https://openalex.org/C2780222073","wikidata":"https://www.wikidata.org/wiki/Q649817","display_name":"Gerbil","level":3,"score":0.5027832984924316},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3290413022041321},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10018482804298401},{"id":"https://openalex.org/C541997718","wikidata":"https://www.wikidata.org/wiki/Q188151","display_name":"Ischemia","level":2,"score":0.0},{"id":"https://openalex.org/C164705383","wikidata":"https://www.wikidata.org/wiki/Q10379","display_name":"Cardiology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13015-017-0097-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0097-9","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0097-9","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:28373894","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28373894","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:e843c8efe97846279444831cdfac9c14","is_oa":true,"landing_page_url":"https://doaj.org/article/e843c8efe97846279444831cdfac9c14","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 12, Iss 1, Pp 1-12 (2017)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5374613","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5374613","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-017-0097-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0097-9","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0097-9","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","score":0.5699999928474426,"display_name":"Decent work and economic growth"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2597444305.pdf","grobid_xml":"https://content.openalex.org/works/W2597444305.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1978814852","https://openalex.org/W2010454899","https://openalex.org/W2027667941","https://openalex.org/W2057253402","https://openalex.org/W2096128575","https://openalex.org/W2097066660","https://openalex.org/W2104677379","https://openalex.org/W2113292893","https://openalex.org/W2118537970","https://openalex.org/W2125266506","https://openalex.org/W2144560237","https://openalex.org/W2163584430","https://openalex.org/W2268029186","https://openalex.org/W2299673938","https://openalex.org/W2411730464","https://openalex.org/W2501688401","https://openalex.org/W2951105277","https://openalex.org/W2952465196","https://openalex.org/W2992755231"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2038909506","https://openalex.org/W2064586431","https://openalex.org/W1977771311","https://openalex.org/W3201075100","https://openalex.org/W2280007336","https://openalex.org/W2067642731","https://openalex.org/W1993625524","https://openalex.org/W2001826608","https://openalex.org/W2474614083"],"abstract_inverted_index":{"While":[0],"<i>Gerbil</i>'s":[1],"performance":[2],"is":[3],"comparable":[4],"to":[5],"existing":[6],"state-of-the-art":[7],"open":[8],"source":[9],"<i>k</i>-mer":[10],"counting":[11],"tools":[12],"for":[13,23],"small":[14],"<i>k</i>":[15],"<":[16],"32,":[17],"it":[18],"vastly":[19],"outperforms":[20],"its":[21],"competitors":[22],"large":[24,32],"<i>k</i>,":[25],"thereby":[26],"enabling":[27],"new":[28],"applications":[29],"which":[30],"require":[31],"values":[33],"of":[34],"<i>k</i>.":[35]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":5}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2017-04-07T00:00:00"}
