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It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/snakemake.googlecode.com.<\/jats:p>\n               <jats:p>Contact: \u00a0johannes.koester@uni-due.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts480","type":"journal-article","created":{"date-parts":[[2012,8,21]],"date-time":"2012-08-21T01:12:25Z","timestamp":1345511545000},"page":"2520-2522","source":"Crossref","is-referenced-by-count":2473,"title":["Snakemake\u2014a scalable bioinformatics workflow engine"],"prefix":"10.1093","volume":"28","author":[{"given":"Johannes","family":"K\u00f6ster","sequence":"first","affiliation":[{"name":"1 Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen and 2Paediatric Oncology, University Childrens Hospital, 45147 Essen, Germany"},{"name":"1 Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen and 2Paediatric Oncology, University Childrens Hospital, 45147 Essen, Germany"}]},{"given":"Sven","family":"Rahmann","sequence":"additional","affiliation":[{"name":"1 Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen and 2Paediatric Oncology, University Childrens Hospital, 45147 Essen, Germany"}]}],"member":"286","published-online":{"date-parts":[[2012,8,20]]},"reference":[{"key":"2023012513143574900_bts480-B1","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1002\/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N","article-title":"An open graph visualization system and its applications to software engineering","volume":"30","author":"Gansner","year":"2000","journal-title":"Software Pract Exper"},{"key":"2023012513143574900_bts480-B2","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biol."},{"key":"2023012513143574900_bts480-B3","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1093\/bioinformatics\/btq524","article-title":"Ruffus: a lightweight Python library for computational pipelines","volume":"26","author":"Goodstadt","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012513143574900_bts480-B4","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nmeth.1809","article-title":"GeneProf: analysis of high-throughput sequencing experiments","volume":"9","author":"Halbritter","year":"2011","journal-title":"Nat. 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