{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T08:03:59Z","timestamp":1774598639474,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T00:00:00Z","timestamp":1662076800000},"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\/100016662","name":"The Carnegie Institution for Science","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100016662","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We developed grenepipe, an all-in-one Snakemake workflow to streamline the data processing from raw high-throughput sequencing data of individuals or populations to genotype variant calls. Our pipeline offers a range of popular software tools within a single configuration file, automatically installs software dependencies, is highly optimized for scalability in cluster environments and runs with a single command.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>grenepipe is published under the GPLv3 and freely available at github.com\/moiexpositoalonsolab\/grenepipe.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac600","type":"journal-article","created":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T13:58:40Z","timestamp":1662127120000},"page":"4809-4811","source":"Crossref","is-referenced-by-count":20,"title":["grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1340-9644","authenticated-orcid":false,"given":"Lucas","family":"Czech","sequence":"first","affiliation":[{"name":"Department of Plant Biology, Carnegie Institution for Science , Stanford, CA 94305, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5711-0700","authenticated-orcid":false,"given":"Moises","family":"Exposito-Alonso","sequence":"additional","affiliation":[{"name":"Department of Plant Biology, Carnegie Institution for Science , Stanford, CA 94305, USA"},{"name":"Department of Global Ecology, Carnegie Institution for Science , Stanford, CA 94305, USA"},{"name":"Department of Biology, Stanford University , Stanford, CA 94305, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,9,2]]},"reference":[{"key":"2023080416563244100_btac600-B1","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2023080416563244100_btac600-B2","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2023080416563244100_btac600-B3","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.3505","article-title":"SpeedSeq: ultra-fast personal genome analysis and interpretation","volume":"12","author":"Chiang","year":"2015","journal-title":"Nat. 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