{"id":"https://openalex.org/W3176045182","doi":"https://doi.org/10.1515/jib-2022-0059","title":"SnakeLines: integrated set of computational pipelines for sequencing reads","display_name":"SnakeLines: integrated set of computational pipelines for sequencing reads","publication_year":2023,"publication_date":"2023-08-21","ids":{"openalex":"https://openalex.org/W3176045182","doi":"https://doi.org/10.1515/jib-2022-0059","mag":"3176045182","pmid":"https://pubmed.ncbi.nlm.nih.gov/37602733"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2022-0059","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2022-0059","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2022-0059/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2022-0059/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003521595","display_name":"Jaroslav Budi\u0161","orcid":"https://orcid.org/0000-0002-8667-6655"},"institutions":[{"id":"https://openalex.org/I4210156920","display_name":"Slovak Centre of Scientific and Technical Information","ror":"https://ror.org/054ys1f07","country_code":"SK","type":"archive","lineage":["https://openalex.org/I4210156920"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]},{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":true,"raw_author_name":"Jaroslav Budi\u0161","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia","Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]},{"raw_affiliation_string":"Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210156920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023863149","display_name":"Werner Krampl","orcid":"https://orcid.org/0000-0003-2567-9753"},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Werner Krampl","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017850074","display_name":"Marcel Kuchar\u00edk","orcid":"https://orcid.org/0000-0002-5373-8282"},"institutions":[{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]},{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Marcel Kuchar\u00edk","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071437834","display_name":"Rastislav Hekel","orcid":"https://orcid.org/0000-0003-1623-9537"},"institutions":[{"id":"https://openalex.org/I4210156920","display_name":"Slovak Centre of Scientific and Technical Information","ror":"https://ror.org/054ys1f07","country_code":"SK","type":"archive","lineage":["https://openalex.org/I4210156920"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]},{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Rastislav Hekel","raw_affiliation_strings":["Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia","Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]},{"raw_affiliation_string":"Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210156920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011426923","display_name":"Adri\u00e1n Goga","orcid":null},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Adri\u00e1n Goga","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Department of Computer Science, Faculty of Mathematics, Physics and Informatics , Comenius University , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Department of Computer Science, Faculty of Mathematics, Physics and Informatics , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018123627","display_name":"Jozef Sitar\u010d\u00edk","orcid":null},"institutions":[{"id":"https://openalex.org/I4210156920","display_name":"Slovak Centre of Scientific and Technical Information","ror":"https://ror.org/054ys1f07","country_code":"SK","type":"archive","lineage":["https://openalex.org/I4210156920"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]},{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Jozef Sitar\u010d\u00edk","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia","Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]},{"raw_affiliation_string":"Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210156920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053616256","display_name":"Michal Lichv\u00e1r","orcid":null},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Michal Lichv\u00e1r","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015836464","display_name":"D\u00e1vid Smo\u013eak","orcid":null},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"D\u00e1vid Smol\u2019ak","raw_affiliation_strings":["Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015196932","display_name":"Miroslav B\u00f6hmer","orcid":"https://orcid.org/0000-0002-9496-5617"},"institutions":[{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]},{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Miroslav B\u00f6hmer","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059632877","display_name":"Andrej Bal\u00e1\u017e","orcid":"https://orcid.org/0000-0002-3113-3389"},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Andrej Bal\u00e1\u017e","raw_affiliation_strings":["Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics , Comenius University , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040960738","display_name":"Franti\u0161ek \u010euri\u0161","orcid":"https://orcid.org/0000-0001-8985-4122"},"institutions":[{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]},{"id":"https://openalex.org/I4210156920","display_name":"Slovak Centre of Scientific and Technical Information","ror":"https://ror.org/054ys1f07","country_code":"SK","type":"archive","lineage":["https://openalex.org/I4210156920"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Franti\u0161ek \u010euri\u0161","raw_affiliation_strings":["Geneton Ltd. , 841 04 Bratislava , Slovakia","Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]},{"raw_affiliation_string":"Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210156920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047760740","display_name":"Juraj Gazdarica","orcid":"https://orcid.org/0000-0002-9042-3589"},"institutions":[{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]},{"id":"https://openalex.org/I4210156920","display_name":"Slovak Centre of Scientific and Technical Information","ror":"https://ror.org/054ys1f07","country_code":"SK","type":"archive","lineage":["https://openalex.org/I4210156920"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Juraj Gazdarica","raw_affiliation_strings":["Geneton Ltd. , 841 04 Bratislava , Slovakia","Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]},{"raw_affiliation_string":"Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210156920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076584994","display_name":"Katar\u00edna \u0160olt\u00fds","orcid":"https://orcid.org/0000-0003-3862-3329"},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Katar\u00edna \u0160oltys","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063713045","display_name":"J\u00e1n Tur\u0148a","orcid":"https://orcid.org/0000-0001-5813-566X"},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]},{"id":"https://openalex.org/I4210156920","display_name":"Slovak Centre of Scientific and Technical Information","ror":"https://ror.org/054ys1f07","country_code":"SK","type":"archive","lineage":["https://openalex.org/I4210156920"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"J\u00e1n Tur\u0148a","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Slovak Centre of Scientific and Technical Information , 811 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210156920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041577194","display_name":"J\u00e1n Radv\u00e1nszky","orcid":"https://orcid.org/0000-0001-9657-1198"},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]},{"id":"https://openalex.org/I4210123996","display_name":"Biomedical Research Center of the Slovak Academy of Sciences","ror":"https://ror.org/02s3ds748","country_code":"SK","type":"facility","lineage":["https://openalex.org/I207624831","https://openalex.org/I4210123996"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"J\u00e1n Radv\u00e1nszky","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia","Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences , 845 05 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]},{"raw_affiliation_string":"Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences , 845 05 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210123996"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085593232","display_name":"Tom\u00e1\u0161 Szemes","orcid":"https://orcid.org/0000-0002-0900-2534"},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]},{"id":"https://openalex.org/I4210155685","display_name":"Geneton (Slovakia)","ror":"https://ror.org/051nezy81","country_code":"SK","type":"company","lineage":["https://openalex.org/I4210155685"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Szemes","raw_affiliation_strings":["Comenius University Science Park , 841 04 Bratislava , Slovakia","Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","Geneton Ltd. , 841 04 Bratislava , Slovakia"],"affiliations":[{"raw_affiliation_string":"Comenius University Science Park , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Department of Molecular Biology, Faculty of Natural Sciences , Comenius University , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I74788687"]},{"raw_affiliation_string":"Geneton Ltd. , 841 04 Bratislava , Slovakia","institution_ids":["https://openalex.org/I4210155685"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":16,"corresponding_author_ids":["https://openalex.org/A5003521595"],"corresponding_institution_ids":["https://openalex.org/I4210155685","https://openalex.org/I4210156920","https://openalex.org/I74788687"],"apc_list":null,"apc_paid":null,"fwci":0.4516,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.65252092,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980999827384949,"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":0.9980999827384949,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.992900013923645,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9887999892234802,"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/computer-science","display_name":"Computer science","score":0.7848894596099854},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5937268137931824},{"id":"https://openalex.org/keywords/massive-parallel-sequencing","display_name":"Massive parallel sequencing","score":0.5076369047164917},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.47528043389320374},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.47384315729141235},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4352933168411255},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.42578989267349243},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.41813182830810547},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.41694965958595276},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38849228620529175},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33156663179397583},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.2141367495059967},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20032215118408203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17616239190101624},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.0901648998260498}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7848894596099854},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5937268137931824},{"id":"https://openalex.org/C192800701","wikidata":"https://www.wikidata.org/wiki/Q6784807","display_name":"Massive parallel sequencing","level":4,"score":0.5076369047164917},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.47528043389320374},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.47384315729141235},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4352933168411255},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.42578989267349243},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.41813182830810547},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.41694965958595276},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38849228620529175},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33156663179397583},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2141367495059967},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20032215118408203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17616239190101624},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0901648998260498},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"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":"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":"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1515/jib-2022-0059","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2022-0059","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2022-0059/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37602733","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37602733","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10757078","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10757078","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10757078/pdf/jib-20-3-jib-2022-0059.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":"J Integr Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:cdd1341e2cfa41c09c30b7750a7d7fcc","is_oa":true,"landing_page_url":"https://doaj.org/article/cdd1341e2cfa41c09c30b7750a7d7fcc","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 20, Iss 3, Pp 0021-6 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2022-0059","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2022-0059","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2022-0059/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G4057535084","display_name":null,"funder_award_id":"PP-COVID-20-0051 (5%)","funder_id":"https://openalex.org/F4320323251","funder_display_name":"Agent\u00fara na Podporu V\u00fdskumu a V\u00fdvoja"},{"id":"https://openalex.org/G6737171669","display_name":null,"funder_award_id":"APVV-20-0472 (5%)","funder_id":"https://openalex.org/F4320323251","funder_display_name":"Agent\u00fara na Podporu V\u00fdskumu a V\u00fdvoja"}],"funders":[{"id":"https://openalex.org/F4320323251","display_name":"Agent\u00fara na Podporu V\u00fdskumu a V\u00fdvoja","ror":"https://ror.org/037nx0e70"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3176045182.pdf"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W2013434113","https://openalex.org/W2036897871","https://openalex.org/W2055043387","https://openalex.org/W2085926377","https://openalex.org/W2086399100","https://openalex.org/W2103441770","https://openalex.org/W2107772251","https://openalex.org/W2110417468","https://openalex.org/W2111281047","https://openalex.org/W2111647009","https://openalex.org/W2114104545","https://openalex.org/W2119180969","https://openalex.org/W2120902911","https://openalex.org/W2127774996","https://openalex.org/W2128711701","https://openalex.org/W2131271579","https://openalex.org/W2131374955","https://openalex.org/W2136207878","https://openalex.org/W2137107630","https://openalex.org/W2152885278","https://openalex.org/W2153325555","https://openalex.org/W2168440186","https://openalex.org/W2170551349","https://openalex.org/W2199980832","https://openalex.org/W2309295884","https://openalex.org/W2310259903","https://openalex.org/W2323851578","https://openalex.org/W2432815617","https://openalex.org/W2466387107","https://openalex.org/W2522185681","https://openalex.org/W2570760970","https://openalex.org/W2577896867","https://openalex.org/W2592811885","https://openalex.org/W2732139758","https://openalex.org/W2737370764","https://openalex.org/W2748728020","https://openalex.org/W2750888327","https://openalex.org/W2763878612","https://openalex.org/W2765745983","https://openalex.org/W2789843538","https://openalex.org/W2794987640","https://openalex.org/W2799170276","https://openalex.org/W2808577271","https://openalex.org/W2808968362","https://openalex.org/W2889664156","https://openalex.org/W2891891121","https://openalex.org/W2897204056","https://openalex.org/W2902028500","https://openalex.org/W2917207851","https://openalex.org/W2919294421","https://openalex.org/W2929354011","https://openalex.org/W2939626517","https://openalex.org/W2940739638","https://openalex.org/W2947747649","https://openalex.org/W2951027231","https://openalex.org/W2951331911","https://openalex.org/W2951563276","https://openalex.org/W2951912016","https://openalex.org/W2952167528","https://openalex.org/W2952654997","https://openalex.org/W2952972032","https://openalex.org/W2963276645","https://openalex.org/W3007653065","https://openalex.org/W3014498785","https://openalex.org/W3084108197","https://openalex.org/W3088710451","https://openalex.org/W3118619395","https://openalex.org/W3121401199","https://openalex.org/W3206515088","https://openalex.org/W3216386097","https://openalex.org/W4225851399","https://openalex.org/W4240187290","https://openalex.org/W4242789727"],"related_works":["https://openalex.org/W3043668926","https://openalex.org/W3036436206","https://openalex.org/W4238948313","https://openalex.org/W4389452281","https://openalex.org/W3111832393","https://openalex.org/W3000916974","https://openalex.org/W3183189600","https://openalex.org/W3134948850","https://openalex.org/W2573498001","https://openalex.org/W2987572536"],"abstract_inverted_index":{"With":[0],"the":[1,47,125,145,175],"rapid":[2,129],"growth":[3],"of":[4,21,49,59,71,93,121,133,147,179],"massively":[5],"parallel":[6],"sequencing":[7,22,78],"technologies,":[8],"still":[9],"more":[10],"laboratories":[11],"are":[12,113],"utilising":[13],"sequenced":[14],"DNA":[15],"fragments":[16],"for":[17,36,76,144],"genomic":[18],"analyses.":[19],"Interpretation":[20],"data":[23],"is,":[24],"however,":[25],"strongly":[26],"dependent":[27],"on":[28,152],"bioinformatics":[29,63,148],"processing,":[30],"which":[31],"is":[32,140,162],"often":[33],"too":[34],"demanding":[35],"clinicians":[37],"and":[38,62,88,99,131,158,170],"researchers":[39],"without":[40],"a":[41,107,141,153],"computational":[42,50,54,72],"background.":[43],"Another":[44],"problem":[45],"represents":[46],"reproducibility":[48,132],"analyses":[51],"across":[52,135],"separated":[53],"centres":[55],"with":[56,97,150],"inconsistent":[57],"versions":[58],"installed":[60],"libraries":[61],"tools.":[64],"We":[65],"propose":[66],"an":[67,94],"easily":[68],"extensible":[69],"set":[70],"pipelines,":[73],"called":[74],"SnakeLines,":[75],"processing":[77],"reads;":[79],"including":[80],"mapping,":[81],"assembly,":[82],"variant":[83],"calling,":[84],"viral":[85],"identification,":[86],"transcriptomics,":[87],"metagenomics":[89],"analysis.":[90],"Individual":[91],"steps":[92],"analysis,":[95],"along":[96],"methods":[98],"their":[100,171],"parameters":[101],"can":[102],"be":[103],"readily":[104],"modified":[105],"in":[106,115,166,174],"single":[108],"configuration":[109],"file.":[110],"Provided":[111],"pipelines":[112],"embedded":[114],"virtual":[116],"environments":[117],"that":[118],"ensure":[119],"isolation":[120],"required":[122],"resources":[123],"from":[124],"host":[126],"operating":[127],"system,":[128],"deployment,":[130],"analysis":[134],"different":[136],"Unix-based":[137],"platforms.":[138],"SnakeLines":[139],"powerful":[142],"framework":[143,161],"automation":[146],"analyses,":[149],"emphasis":[151],"simple":[154],"set-up,":[155],"modifications,":[156],"extensibility,":[157],"reproducibility.":[159],"The":[160],"already":[163],"routinely":[164],"used":[165],"various":[167],"research":[168],"projects":[169],"applications,":[172],"especially":[173],"Slovak":[176],"national":[177],"surveillance":[178],"SARS-CoV-2.":[180]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
