{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T18:26:50Z","timestamp":1775845610579,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,12,28]],"date-time":"2016-12-28T00:00:00Z","timestamp":1482883200000},"content-version":"vor","delay-in-days":1024,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.<\/jats:p>\n               <jats:p>Availability and implementation: Orione is available online at http:\/\/orione.crs4.it .<\/jats:p>\n               <jats:p>Contact: \u00a0gianmauro.cuccuru@crs4.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu135","type":"journal-article","created":{"date-parts":[[2014,3,12]],"date-time":"2014-03-12T00:16:49Z","timestamp":1394583409000},"page":"1928-1929","source":"Crossref","is-referenced-by-count":169,"title":["Orione, a web-based framework for NGS analysis in microbiology"],"prefix":"10.1093","volume":"30","author":[{"given":"Gianmauro","family":"Cuccuru","sequence":"first","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]},{"given":"Massimiliano","family":"Orsini","sequence":"additional","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]},{"given":"Andrea","family":"Pinna","sequence":"additional","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]},{"given":"Andrea","family":"Sbardellati","sequence":"additional","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]},{"given":"Nicola","family":"Soranzo","sequence":"additional","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]},{"given":"Antonella","family":"Travaglione","sequence":"additional","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]},{"given":"Paolo","family":"Uva","sequence":"additional","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]},{"given":"Gianluigi","family":"Zanetti","sequence":"additional","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]},{"given":"Giorgio","family":"Fotia","sequence":"additional","affiliation":[{"name":"CRS4, Science and Technology Park Polaris, Piscina Manna, 09010 Pula (CA), Italy"}]}],"member":"286","published-online":{"date-parts":[[2014,3,10]]},"reference":[{"key":"2023012711182078400_btu135-B1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nmeth.1896","article-title":"OMERO: flexible, model-driven data management for experimental biology","volume":"9","author":"Allan","year":"2012","journal-title":"Nat. Methods"},{"key":"2023012711182078400_btu135-B2","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"2023012711182078400_btu135-B3","doi-asserted-by":"crossref","first-page":"1233158","DOI":"10.1126\/science.1233158","article-title":"Lentiviral hematopoietic stem cell gene therapy benefits metachromatic leukodystrophy","volume":"341","author":"Biffi","year":"2013","journal-title":"Science"},{"key":"2023012711182078400_btu135-B4","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/bioinformatics\/btq683","article-title":"Scaffolding pre-assembled contigs using SSPACE","volume":"27","author":"Boetzer","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012711182078400_btu135-B5","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1093\/bioinformatics\/btr046","article-title":"Shrimp2: sensitive yet practical short read mapping","volume":"27","author":"David","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012711182078400_btu135-B6","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1186\/1471-2105-11-345","article-title":"SOPRA: scaffolding algorithm for paired reads via statistical optimization","volume":"11","author":"Dayarian","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012711182078400_btu135-B7","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","article-title":"Identifying bacterial genes and endosymbiont DNA with Glimmer","volume":"23","author":"Delcher","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012711182078400_btu135-B8","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":"2023012711182078400_btu135-B9","volume-title":"Improved pairwise alignment of genomic DNA","author":"Harris","year":"2007"},{"key":"2023012711182078400_btu135-B10","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1101\/gr.072033.107","article-title":"De novo\n               bacterial genome sequencing: millions of very short reads assembled on a desktop computer","volume":"18","author":"Hernandez","year":"2008","journal-title":"Genome Res."},{"key":"2023012711182078400_btu135-B11","doi-asserted-by":"crossref","first-page":"e7767","DOI":"10.1371\/journal.pone.0007767","article-title":"BFAST: an alignment tool for large scale genome resequencing","volume":"4","author":"Homer","year":"2009","journal-title":"PLoS One"},{"key":"2023012711182078400_btu135-B12","first-page":"656","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012711182078400_btu135-B13","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2023012711182078400_btu135-B14","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012711182078400_btu135-B15","doi-asserted-by":"crossref","DOI":"10.1145\/2287016.2287026","article-title":"SNP genotype calling with MapReduce","volume-title":"Proceedings of The Third International Workshop on MapReduce and its Applications","author":"Leo","year":"2012"},{"key":"2023012711182078400_btu135-B16","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711182078400_btu135-B17","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/bioinformatics\/btn025","article-title":"SOAP: short oligonucleotide alignment program","volume":"24","author":"Li","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012711182078400_btu135-B18","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/nrmicro2850","article-title":"High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity","volume":"10","author":"Loman","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"2023012711182078400_btu135-B19","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012711182078400_btu135-B20","doi-asserted-by":"crossref","first-page":"127","DOI":"10.4137\/EBO.S11250","article-title":"EDGE-pro: estimated degree of gene expression in prokaryotic genomes","volume":"9","author":"Magoc","year":"2013","journal-title":"Evol. Bioinform. Online"},{"key":"2023012711182078400_btu135-B21","doi-asserted-by":"crossref","first-page":"e155","DOI":"10.1093\/nar\/gks678","article-title":"MetaVelvet: an extension of Velvet assembler to \n              de novo\n               metagenome assembly from short sequence reads","volume":"40","author":"Namiki","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012711182078400_btu135-B22","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1186\/1471-2105-12-385","article-title":"Interactive metagenomic visualization in a web browser","volume":"12","author":"Ondov","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012711182078400_btu135-B23","doi-asserted-by":"crossref","first-page":"23","DOI":"10.14806\/ej.19.A.626","article-title":"Automated and traceable processing for large-scale high-throughput sequencing facilities","volume":"19","author":"Pireddu","year":"2013","journal-title":"EMBnet. J."},{"key":"2023012711182078400_btu135-B24","first-page":"1","article-title":"iRODS primer: integrated rule-oriented data system","volume-title":"Synthesis Lectures on Information Concepts, Retrieval, and Services","author":"Rajasekar","year":"2010"},{"key":"2023012711182078400_btu135-B25","doi-asserted-by":"crossref","first-page":"i188","DOI":"10.1093\/bioinformatics\/bts219","article-title":"SEQuel: improving the accuracy of genome assemblies","volume":"28","author":"Ronen","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711182078400_btu135-B26","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nmeth.2066","article-title":"Metagenomic microbial community profiling using unique clade-specific marker genes","volume":"9","author":"Segata","year":"2012","journal-title":"Nat. Methods"},{"key":"2023012711182078400_btu135-B27","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","article-title":"ABySS: a parallel assembler for short read sequence data","volume":"19","author":"Simpson","year":"2009","journal-title":"Genome Res."},{"key":"2023012711182078400_btu135-B28","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1093\/bioinformatics\/btl629","article-title":"Assembling millions of short DNA sequences using SSAKE","volume":"23","author":"Warren","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012711182078400_btu135-B29","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for \n              de novo\n               short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."},{"key":"2023012711182078400_btu135-B30","doi-asserted-by":"crossref","first-page":"e132","DOI":"10.1093\/nar\/gkq275","article-title":"Ab initio\n               gene identification in metagenomic sequences","volume":"38","author":"Zhu","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/13\/1928\/48925013\/bioinformatics_30_13_1928.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/13\/1928\/48925013\/bioinformatics_30_13_1928.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:54:27Z","timestamp":1674820467000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/13\/1928\/2422241"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,3,10]]},"references-count":30,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2014,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu135","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,7,1]]},"published":{"date-parts":[[2014,3,10]]}}}