{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,19]],"date-time":"2026-07-19T05:14:35Z","timestamp":1784438075428,"version":"3.55.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,12,28]],"date-time":"2016-12-28T00:00:00Z","timestamp":1482883200000},"content-version":"vor","delay-in-days":803,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,15]]},"abstract":"<jats:p>Motivation: PIWI-interacting RNAs (piRNAs), 23\u201336 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial computational skills. Additionally, researchers may analyze and interpret the same data differently, generating results that are difficult to reconcile. To address these issues, we developed a coordinated set of pipelines, \u2018piPipes\u2019, to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field.<\/jats:p>\n               <jats:p>Supplementary information: Supplementary information, including flowcharts and example figures for each pipeline, are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Availability and implementation: piPipes is implemented in Bash, C++, Python, Perl and R. piPipes is free, open-source software distributed under the GPLv3 license and is available at http:\/\/bowhan.github.io\/piPipes\/.<\/jats:p>\n               <jats:p>Contact: Phillip.Zamore@umassmed.edu or Zhiping.Weng@umassmed.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu647","type":"journal-article","created":{"date-parts":[[2014,10,18]],"date-time":"2014-10-18T02:34:38Z","timestamp":1413599678000},"page":"593-595","source":"Crossref","is-referenced-by-count":141,"title":["piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing"],"prefix":"10.1093","volume":"31","author":[{"given":"Bo W.","family":"Han","sequence":"first","affiliation":[{"name":"1 \u00a01RNA Therapeutics Institute, 2Howard Hughes Medical Institute, 3Department of Biochemistry & Molecular Pharmacology and 4Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"1 \u00a01RNA Therapeutics Institute, 2Howard Hughes Medical Institute, 3Department of Biochemistry & Molecular Pharmacology and 4Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phillip D.","family":"Zamore","sequence":"additional","affiliation":[{"name":"1 \u00a01RNA Therapeutics Institute, 2Howard Hughes Medical Institute, 3Department of Biochemistry & Molecular Pharmacology and 4Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiping","family":"Weng","sequence":"additional","affiliation":[{"name":"1 \u00a01RNA Therapeutics Institute, 2Howard Hughes Medical Institute, 3Department of Biochemistry & Molecular Pharmacology and 4Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,10,17]]},"reference":[{"key":"2023020108564811900_btu647-B18","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq - A Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020108564811900_btu647-B1","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.cell.2007.01.043","article-title":"Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila","volume":"6","author":"Brennecke","year":"2007","journal-title":"Cell"},{"key":"2023020108564811900_btu647-B2","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1363","article-title":"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation","volume":"9","author":"Chen","year":"2009","journal-title":"Nat. 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