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New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well as microRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNA-seq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.<\/jats:p>","DOI":"10.1093\/nar\/gkz415","type":"journal-article","created":{"date-parts":[[2019,5,14]],"date-time":"2019-05-14T07:40:49Z","timestamp":1557819649000},"page":"W530-W535","source":"Crossref","is-referenced-by-count":172,"title":["sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression"],"prefix":"10.1093","volume":"47","author":[{"given":"Ernesto","family":"Aparicio-Puerta","sequence":"first","affiliation":[{"name":"Dpto. de Gen\u00e9tica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s\/n, 18071 Granada, Spain"},{"name":"Lab. de Bioinform\u00e1tica, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), PTS, Avda. del Conocimiento s\/n, 18100 Granada. Spain"},{"name":"Department of Human Anatomy and Embryology, Institute of Biopathology and Regenerative Medicine, Excellence Research Unit \u2018Modeling Nature' (MNat), University of Granada, Granada, Spain"},{"name":"Instituto de Investigaci\u00f3n Biosanitaria ibs.GRANADA, University Hospitals of Granada-University of Granada, Spain; Conocimiento s\/n, 18100 Granada. Spain"}]},{"given":"Ricardo","family":"Lebr\u00f3n","sequence":"additional","affiliation":[{"name":"Dpto. de Gen\u00e9tica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s\/n, 18071 Granada, Spain"},{"name":"Lab. de Bioinform\u00e1tica, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), PTS, Avda. del Conocimiento s\/n, 18100 Granada. Spain"}]},{"given":"Antonio","family":"Rueda","sequence":"additional","affiliation":[{"name":"Genomics England, Charterhouse Square, London EC1M 6BQ, UK"}]},{"given":"Cristina","family":"G\u00f3mez-Mart\u00edn","sequence":"additional","affiliation":[{"name":"Dpto. de Gen\u00e9tica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s\/n, 18071 Granada, Spain"},{"name":"Lab. de Bioinform\u00e1tica, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), PTS, Avda. del Conocimiento s\/n, 18100 Granada. Spain"}]},{"given":"Stavros","family":"Giannoukakos","sequence":"additional","affiliation":[{"name":"Dpto. de Gen\u00e9tica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s\/n, 18071 Granada, Spain"},{"name":"Lab. de Bioinform\u00e1tica, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), PTS, Avda. del Conocimiento s\/n, 18100 Granada. Spain"}]},{"given":"David","family":"Jaspez","sequence":"additional","affiliation":[{"name":"Dpto. de Gen\u00e9tica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s\/n, 18071 Granada, Spain"}]},{"given":"Jos\u00e9 Mar\u00eda","family":"Medina","sequence":"additional","affiliation":[{"name":"Dpto. de Gen\u00e9tica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s\/n, 18071 Granada, Spain"},{"name":"Lab. de Bioinform\u00e1tica, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), PTS, Avda. del Conocimiento s\/n, 18100 Granada. Spain"}]},{"given":"Andreja","family":"Zubkovic","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, University of Rijeka, Croatia"}]},{"given":"Igor","family":"Jurak","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, University of Rijeka, Croatia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0352-3037","authenticated-orcid":false,"given":"Bastian","family":"Fromm","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden"}]},{"given":"Juan Antonio","family":"Marchal","sequence":"additional","affiliation":[{"name":"Department of Human Anatomy and Embryology, Institute of Biopathology and Regenerative Medicine, Excellence Research Unit \u2018Modeling Nature' (MNat), University of Granada, Granada, Spain"},{"name":"Instituto de Investigaci\u00f3n Biosanitaria ibs.GRANADA, University Hospitals of Granada-University of Granada, Spain; Conocimiento s\/n, 18100 Granada. Spain"}]},{"given":"Jos\u00e9","family":"Oliver","sequence":"additional","affiliation":[{"name":"Dpto. de Gen\u00e9tica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s\/n, 18071 Granada, Spain"},{"name":"Lab. de Bioinform\u00e1tica, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), PTS, Avda. del Conocimiento s\/n, 18100 Granada. Spain"}]},{"given":"Michael","family":"Hackenberg","sequence":"additional","affiliation":[{"name":"Dpto. de Gen\u00e9tica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s\/n, 18071 Granada, Spain"},{"name":"Lab. de Bioinform\u00e1tica, Centro de Investigaci\u00f3n Biom\u00e9dica (CIBM), PTS, Avda. del Conocimiento s\/n, 18100 Granada. Spain"},{"name":"Instituto de Investigaci\u00f3n Biosanitaria ibs.GRANADA, University Hospitals of Granada-University of Granada, Spain; Conocimiento s\/n, 18100 Granada. 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