{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T17:32:11Z","timestamp":1746207131228},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,8]],"date-time":"2019-08-08T00:00:00Z","timestamp":1565222400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Spanish Ministry of Economy, Industry and Competitiveness"},{"name":"Centro de Excelencia Severo Ochoa","award":["SEV-2012-0208"]},{"name":"Catalan Research Agency","award":["SGR857"]},{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["ERC-2016-724173"]},{"name":"Marie Sklodowska-Curie","award":["H2020-MSCA-ITN-2014-642095"]},{"name":"INB","award":["PT17\/0009\/0023","\u2013","ISCIII-SGEFI\/ERDF"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing genetic material from divergent organisms. A crucial step in these studies is identifying from which organism each sequencing read originated, and the experimental design should be directed to minimize biases caused by cross-mapping of reads to incorrect source genomes. Additionally, pooling of sufficiently different genetic material into a single sequencing library could significantly reduce experimental costs but requires careful planning and assessment of the impact of cross-mapping. Having these applications in mind we designed Crossmapper, the first to our knowledge tool able to assess cross-mapping prior to sequencing, therefore allowing optimization of experimental design.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Using any combination of reference genomes, Crossmapper performs read simulation and back-mapping of those reads to the pool of references, quantifies and reports the cross-mapping rates for each organism. Crossmapper performs these analyses with numerous user-specified parameters, including, among others, read length, read layout, coverage, mapping parameters, genomic or transcriptomic data. Additionally, it outputs the results in highly interactive and publication-ready reports. This allows the user to perform multiple comparisons at once and choose the experimental setup minimizing cross-mapping rates. Moreover, Crossmapper can be used for resource optimization in sequencing facilities by pooling different samples into one sequencing library.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n Crossmapper is a command line tool implemented in Python 3.6 and available as a conda package, allowing effortless installation. The source code, detailed information and a step-by-step tutorial is available at our GitHub page https:\/\/github.com\/Gabaldonlab\/crossmapper.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz626","type":"journal-article","created":{"date-parts":[[2019,8,6]],"date-time":"2019-08-06T19:17:18Z","timestamp":1565119038000},"page":"925-927","source":"Crossref","is-referenced-by-count":17,"title":["CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies"],"prefix":"10.1093","volume":"36","author":[{"given":"Hrant","family":"Hovhannisyan","sequence":"first","affiliation":[{"name":"Centre for Genomic Regulation, Department of Bioinformatics and Genomics , The Barcelona Institute of Science and Technology, Barcelona, Spain"},{"name":"Department of Experimental and Health Sciences , Universitat Pompeu Fabra, Barcelona, Spain"},{"name":"Barcelona Supercomputing Centre (BSC-CNS) and Institute for Research in Biomedicine (IRB) , Barcelona, Spain"}]},{"given":"Ahmed","family":"Hafez","sequence":"additional","affiliation":[{"name":"Department of Experimental and Health Sciences , Universitat Pompeu Fabra, Barcelona, Spain"},{"name":"Biotechvana S.L., Parc Cient\u00edfic Universitat de Val\u00e8ncia , Valencia, Spain"},{"name":"Faculty of Computers and Information, Minia University , Minia, Egypt"}]},{"given":"Carlos","family":"Llorens","sequence":"additional","affiliation":[{"name":"Biotechvana S.L., Parc Cient\u00edfic Universitat de Val\u00e8ncia , Valencia, Spain"}]},{"given":"Toni","family":"Gabald\u00f3n","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation, Department of Bioinformatics and Genomics , The Barcelona Institute of Science and Technology, Barcelona, Spain"},{"name":"Department of Experimental and Health Sciences , Universitat Pompeu Fabra, Barcelona, Spain"},{"name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats, Barcelona , Spain"},{"name":"Barcelona Supercomputing Centre (BSC-CNS) and Institute for Research in Biomedicine (IRB) , Barcelona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2019,8,8]]},"reference":[{"key":"2023013110093161900_btz626-B1","volume-title":"Elife","author":"Burns","year":"2017"},{"key":"2023013110093161900_btz626-B2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013110093161900_btz626-B3","doi-asserted-by":"crossref","first-page":"8445","DOI":"10.1128\/AEM.02690-15","article-title":"Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing","volume":"81","author":"Gonz\u00e1lez-Torres","year":"2015","journal-title":"Appl. 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