{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:55Z","timestamp":1772138035340,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2020,12,26]],"date-time":"2020-12-26T00:00:00Z","timestamp":1608940800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004063","name":"Knut and Alice Wallenberg foundation","doi-asserted-by":"publisher","award":["2016.0063"],"award-info":[{"award-number":["2016.0063"]}],"id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish research Council","doi-asserted-by":"publisher","award":["2018-02855"],"award-info":[{"award-number":["2018-02855"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container https:\/\/hub.docker.com\/repository\/docker\/snandids\/prokseq-v2.0, or can be used through Anaconda: https:\/\/anaconda.org\/snandiDS\/prokseq. The code is available on Github: https:\/\/github.com\/snandiDS\/prokseq and a detailed user documentation, including a manual and tutorial can be found at https:\/\/prokseqV20.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\/btaa1063","type":"journal-article","created":{"date-parts":[[2020,12,12]],"date-time":"2020-12-12T01:14:46Z","timestamp":1607735686000},"page":"126-128","source":"Crossref","is-referenced-by-count":19,"title":["ProkSeq for complete analysis of RNA-Seq data from prokaryotes"],"prefix":"10.1093","volume":"37","author":[{"given":"A K M Firoj","family":"Mahmud","sequence":"first","affiliation":[{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 Centre for Microbial Research (UCMR), Department of Molecular Biology, Ume\u00e5 University , SE-901 87 Ume\u00e5, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3053-0796","authenticated-orcid":false,"given":"Nicolas","family":"Delhomme","sequence":"additional","affiliation":[{"name":"Department of Forest Genetics and Plant Physiology, Ume\u00e5 Plant Science Centre (UPSC), Swedish University of Agricultural Sciences , Ume\u00e5, Sweden"}]},{"given":"Soumyadeep","family":"Nandi","sequence":"additional","affiliation":[{"name":"Amity Institute of Integrative Sciences and Health, Amity University Haryana , Gurgaon, 122413 Haryana, India"}]},{"given":"Maria","family":"F\u00e4llman","sequence":"additional","affiliation":[{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 Centre for Microbial Research (UCMR), Department of Molecular Biology, Ume\u00e5 University , SE-901 87 Ume\u00e5, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2020,12,26]]},"reference":[{"key":"2023051510474831700_btaa1063-B1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13040-017-0150-8","article-title":"RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study","volume":"10","author":"Berghoff","year":"2017","journal-title":"BioData Min"},{"key":"2023051510474831700_btaa1063-B2","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s12859-017-1469-3","article-title":"AfterQC: automatic filtering, trimming, error removing and quality control for fastq data","volume":"18","author":"Chen","year":"2017","journal-title":"BMC Bioinf"},{"key":"2023051510474831700_btaa1063-B3","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.mib.2014.11.011","article-title":"Quantitative bacterial transcriptomics with RNA-seq","volume":"23","author":"Creecy","year":"2015","journal-title":"Curr. 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