{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T22:13:50Z","timestamp":1782339230246,"version":"3.54.5"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2018,7,17]],"date-time":"2018-07-17T00:00:00Z","timestamp":1531785600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2015-03443_VR"],"award-info":[{"award-number":["2015-03443_VR"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The accurate in silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation of computational needs within a project. Unfortunately, most current read simulators are either not suited for metagenomics, out of date or relatively poorly documented. In this article, we describe InSilicoSeq, a software package to simulate metagenomic Illumina sequencing data. InsilicoSeq has a simple command-line interface and extensive documentation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>InSilicoSeq is implemented in Python and capable of simulating realistic Illumina (meta) genomic data in a parallel fashion with sensible default parameters.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code and documentation are available under the MIT license at https:\/\/github.com\/HadrienG\/InSilicoSeq and https:\/\/insilicoseq.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\/bty630","type":"journal-article","created":{"date-parts":[[2018,7,14]],"date-time":"2018-07-14T17:43:43Z","timestamp":1531590223000},"page":"521-522","source":"Crossref","is-referenced-by-count":252,"title":["Simulating Illumina metagenomic data with InSilicoSeq"],"prefix":"10.1093","volume":"35","author":[{"given":"Hadrien","family":"Gourl\u00e9","sequence":"first","affiliation":[{"name":"Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SLU-Global Bioinformatics Centre"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oskar","family":"Karlsson-Lindsj\u00f6","sequence":"additional","affiliation":[{"name":"Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliette","family":"Hayer","sequence":"additional","affiliation":[{"name":"Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SLU-Global Bioinformatics Centre"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik","family":"Bongcam-Rudloff","sequence":"additional","affiliation":[{"name":"Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SLU-Global Bioinformatics Centre"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,7,19]]},"reference":[{"key":"2023013107245920200_bty630-B1","doi-asserted-by":"crossref","first-page":"e94.","DOI":"10.1093\/nar\/gks251","article-title":"Grinder: a versatile amplicon and shotgun sequence simulator","volume":"40","author":"Angly","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023013107245920200_bty630-B2","doi-asserted-by":"crossref","first-page":"459.","DOI":"10.1038\/nrg.2016.57","article-title":"A comparison of tools for the simulation of genomic next-generation sequencing data","volume":"17","author":"Escalona","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023013107245920200_bty630-B3","doi-asserted-by":"crossref","first-page":"518","DOI":"10.2307\/1317899","article-title":"Teaching social statistics with simulated data","volume":"19","author":"Halley","year":"1991","journal-title":"Teach. Sociol"},{"key":"2023013107245920200_bty630-B4","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1093\/bioinformatics\/bts187","article-title":"pIRS: profile-based illumina pair-end reads simulator","volume":"28","author":"Hu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023013107245920200_bty630-B5","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"ART: a next-generation sequencing read simulator","volume":"28","author":"Huang","year":"2012","journal-title":"Bioinformatics"},{"key":"2023013107245920200_bty630-B6","doi-asserted-by":"crossref","first-page":"e75448","DOI":"10.1371\/journal.pone.0075448","article-title":"NeSSM: a next-generation sequencing simulator for metagenomics","volume":"8","author":"Jia","year":"2013","journal-title":"PLoS One"},{"key":"2023013107245920200_bty630-B7","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1186\/1471-2105-15-S9-S14","article-title":"A better sequence-read simulator program for metagenomics","volume":"15","author":"Johnson","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023013107245920200_bty630-B8","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":"2023013107245920200_bty630-B9","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013107245920200_bty630-B10","article-title":"FunctionSIM","author":"Lingling","year":"2014"},{"key":"2023013107245920200_bty630-B11","doi-asserted-by":"crossref","first-page":"e1005265","DOI":"10.1371\/journal.pcbi.1005265","article-title":"Ten simple rules for developing usable software in computational biology","volume":"13","author":"List","year":"2017","journal-title":"PLoS Comput. Biol"},{"key":"2023013107245920200_bty630-B12","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1471-2164-13-74","article-title":"GemSIM: general, error-model based simulator of next-generation sequencing data","volume":"13","author":"McElroy","year":"2012","journal-title":"BMC Genomics"},{"key":"2023013107245920200_bty630-B13","doi-asserted-by":"crossref","first-page":"e3373","DOI":"10.1371\/journal.pone.0003373","article-title":"MetaSim\u2014a sequencing simulator for genomics and metagenomics","volume":"3","author":"Richter","year":"2008","journal-title":"PLoS One"},{"key":"2023013107245920200_bty630-B14","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1093\/bib\/bbr035","article-title":"A toolbox for developing bioinformatics software","volume":"13","author":"Rother","year":"2012","journal-title":"Brief. Bioinform"},{"key":"2023013107245920200_bty630-B15","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1186\/1756-0500-7-533","article-title":"FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets","volume":"7","author":"Shcherbina","year":"2014","journal-title":"BMC Res. Notes"},{"key":"2023013107245920200_bty630-B16","author":"Silverman","year":"1986"},{"key":"2023013107245920200_bty630-B17","doi-asserted-by":"crossref","first-page":"e1001745","DOI":"10.1371\/journal.pbio.1001745","article-title":"Best practices for scientific computing","volume":"12","author":"Wilson","year":"2014","journal-title":"PLoS Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/3\/521\/48965504\/bioinformatics_35_3_521.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/3\/521\/48965504\/bioinformatics_35_3_521.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T10:19:23Z","timestamp":1675160363000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/3\/521\/5055123"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,7,19]]},"references-count":17,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2019,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty630","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,2,1]]},"published":{"date-parts":[[2018,7,19]]}}}