CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies

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• dc.contributor.author Hovhannisyan, Hrant, 1992-
• dc.contributor.author Hafez Khafaga, Ahmed Ibrahem, 1987-
• dc.contributor.author Llorens, Carlos, 1968-
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.date.accessioned 2020-03-17T07:33:35Z
• dc.date.available 2020-03-17T07:33:35Z
• dc.date.issued 2020
• dc.description.abstract MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
• dc.description.sponsorship This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) for the EMBL partnership and the grant ‘Centro de Excelencia Severo Ochoa’ SEV-2012-0208 cofounded by European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857 and grants from the European Union’s Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173 and the Marie Sklodowska-Curie grant agreement No H2020-MSCA-ITN-2014-642095. The group also receives support from a INB Grant (PT17/0009/0023–ISCIII-SGEFI/ERDF)
• dc.format.mimetype application/pdf
• dc.identifier.citation Hovhannisyan H, Hafez A, Llorens C, Gabaldón T. CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies. Bioinformatics. 2020 Feb 1; 36(3): 925-927. DOI: 10.1093/bioinformatics/btz626
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btz626
• dc.identifier.issn 1367-4803
• dc.identifier.uri http://hdl.handle.net/10230/43908
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Bioinformatics. 2020 Feb 1; 36(3): 925-7
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/724173
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/642095
• dc.rights © 2019 Hrant Hovhannisyan et al. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License,which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.other Anàlisis de seqüències
• dc.subject.other Genètica
• dc.subject.other Genomes
• dc.title CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion