{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,4]],"date-time":"2022-04-04T01:13:24Z","timestamp":1649034804034},"reference-count":12,"publisher":"Springer Science and Business Media LLC","issue":"S9","license":[{"start":{"date-parts":[[2019,11,1]],"date-time":"2019-11-01T00:00:00Z","timestamp":1572566400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,11,22]],"date-time":"2019-11-22T00:00:00Z","timestamp":1574380800000},"content-version":"vor","delay-in-days":21,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set.<\/jats:p>\n                <jats:p>Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query.<\/jats:p>\n                <jats:p>Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs\/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-019-2887-1","type":"journal-article","created":{"date-parts":[[2019,11,22]],"date-time":"2019-11-22T10:02:38Z","timestamp":1574416958000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data"],"prefix":"10.1186","volume":"20","author":[{"given":"Mattia","family":"Dalsass","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Margherita","family":"Bodini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Lambert","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-C\u00e9cile","family":"Mortier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Romanelli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Duccio","family":"Medini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Muzzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Brozzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,11,22]]},"reference":[{"issue":"10","key":"2887_CR1","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1038\/nrmicro3093","volume":"11","author":"MCJ Maiden","year":"2013","unstructured":"Maiden MCJ, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford Sa, Jolley Ka, McCarthy ND. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013;11(10):728\u201336. https:\/\/doi.org\/10.1038\/nrmicro3093.","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"2887_CR2","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1186\/1471-2105-11-595","volume":"11","author":"KA Jolley","year":"2010","unstructured":"Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11(1):595. https:\/\/doi.org\/10.1186\/1471-2105-11-595.","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"2887_CR3","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13073-014-0090-6","volume":"6","author":"M Inouye","year":"2014","unstructured":"Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome medicine. 2014;6(11):90. https:\/\/doi.org\/10.1186\/s13073-014-0090-6.","journal-title":"Genome medicine"},{"issue":"September 2016","key":"2887_CR4","doi-asserted-by":"publisher","first-page":"586","DOI":"10.1093\/bioinformatics\/btw586","volume":"33","author":"A Gupta","year":"2016","unstructured":"Gupta A, Jordan IK, Rishishwar L. stringMLST: a fast k-mer based tool for multi locus sequence typing. Bioinformatics (Oxford, England). 2016;33(September 2016):586. https:\/\/doi.org\/10.1093\/bioinformatics\/btw586.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"6","key":"2887_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1004753","volume":"12","author":"B Brankovics","year":"2016","unstructured":"Brankovics B, Zhang H, van Diepeningen AD, van der Lee TAJ, Waalwijk C, de Hoog GS. GRAbB: selective assembly of genomic regions, a new niche for genomic research. 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J Comput Biol. 2012;19(5):455\u201377. https:\/\/doi.org\/10.1089\/cmb.2012.0021.","journal-title":"J Comput Biol"},{"issue":"5","key":"2887_CR8","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107.0209100","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821\u20139. https:\/\/doi.org\/10.1101\/gr.074492.107.0209100.","journal-title":"Genome Res"},{"key":"2887_CR9","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. 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J Mol Biol [Internet]. 1990;215:403\u2013410.","journal-title":"Journal of Molecular Biology"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2887-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2887-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2887-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,21]],"date-time":"2020-11-21T00:15:09Z","timestamp":1605917709000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2887-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11]]},"references-count":12,"journal-issue":{"issue":"S9","published-print":{"date-parts":[[2019,11]]}},"alternative-id":["2887"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2887-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11]]},"assertion":[{"value":"12 April 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 May 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 November 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"AM, AB, DM, CGL and MCM were employees of GSK group of companies at the time of the study. MB, at the time of the study, was an employee of Randstad Italia spa, working as a contractor for GSK.MD is a PhD student at the University of Turin and participates in a postgraduate studentship program at GSK.MR was an undergraduate student of the University of Siena at the time of the study and supervised by GSK group.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"347"}}