{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T08:50:25Z","timestamp":1769244625725,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,6,13]],"date-time":"2019-06-13T00:00:00Z","timestamp":1560384000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Germany's Excellence Strategy EXC","award":["22167-390884018"],"award-info":[{"award-number":["22167-390884018"]}]},{"DOI":"10.13039\/501100004189","name":"Max Planck Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Long-read third-generation nanopore sequencing enables researchers to now address a range of questions that are difficult to tackle with short read approaches. The rapidly expanding user base and continuously increasing throughput have sparked the development of a growing number of specialized analysis tools. However, streamlined processing of nanopore datasets using reproducible and transparent workflows is still lacking. Here we present Nanopype, a nanopore data processing pipeline that integrates a diverse set of established bioinformatics software while maintaining consistent and standardized output formats. Seamless integration into compute cluster environments makes the framework suitable for high-throughput applications. As a result, Nanopype facilitates comparability of nanopore data analysis workflows and thereby should enhance the reproducibility of biological insights.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/giesselmann\/nanopype, https:\/\/nanopype.readthedocs.io.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz461","type":"journal-article","created":{"date-parts":[[2019,6,7]],"date-time":"2019-06-07T19:11:45Z","timestamp":1559934705000},"page":"4770-4772","source":"Crossref","is-referenced-by-count":12,"title":["Nanopype: a modular and scalable nanopore data processing pipeline"],"prefix":"10.1093","volume":"35","author":[{"given":"Pay","family":"Giesselmann","sequence":"first","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"}]},{"given":"Sara","family":"Hetzel","sequence":"additional","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"}]},{"given":"Franz-Josef","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"},{"name":"Department of Psychiatry and Psychotherapy, Zentrum f\u00fcr Integrative Psychiatrie gGmbH, Universit\u00e4tsklinikum Schleswig-Holstein , Campus Kiel, Kiel, Germany"}]},{"given":"Alexander","family":"Meissner","sequence":"additional","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"}]},{"given":"Helene","family":"Kretzmer","sequence":"additional","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,6,13]]},"reference":[{"key":"2023013108342793400_btz461-B1","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","article-title":"BigWig and BigBed: enabling browsing of large distributed datasets","volume":"26","author":"Kent","year":"2010","journal-title":"Bioinformatics"},{"key":"2023013108342793400_btz461-B2","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake\u2014a scalable bioinformatics workflow engine","volume":"28","author":"K\u00f6ster","year":"2012","journal-title":"Bioinformatics"},{"key":"2023013108342793400_btz461-B3","first-page":"7","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"1","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2023013108342793400_btz461-B4","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023013108342793400_btz461-B5","first-page":"1256","article-title":"Nanopore sequencing data analysis: state of the art, applications and challenges","volume":"19","author":"Magi","year":"2018","journal-title":"Brief. 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