FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies

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  • dc.contributor.author Miravet Verde, Samuel, 1992-
  • dc.contributor.author Burgos, Raul
  • dc.contributor.author Delgado Blanco, Javier
  • dc.contributor.author Lluch-Senar, Maria 1982-
  • dc.contributor.author Serrano Pubull, Luis, 1982-
  • dc.date.accessioned 2020-10-29T06:55:25Z
  • dc.date.available 2020-10-29T06:55:25Z
  • dc.date.issued 2020
  • dc.description.abstract Transposon sequencing is commonly applied for identifying the minimal set of genes required for cellular life; a major challenge in fields such as evolutionary or synthetic biology. However, the scientific community has no standards at the level of processing, treatment, curation and analysis of this kind data. In addition, we lack knowledge about artifactual signals and the requirements a dataset has to satisfy to allow accurate prediction. Here, we have developed FASTQINS, a pipeline for the detection of transposon insertions, and ANUBIS, a library of functions to evaluate and correct deviating factors known and uncharacterized until now. ANUBIS implements previously defined essentiality estimate models in addition to new approaches with advantages like not requiring a training set of genes to predict general essentiality. To highlight the applicability of these tools, and provide a set of recommendations on how to analyze transposon sequencing data, we performed a comprehensive study on artifacts corrections and essentiality estimation at a 1.5-bp resolution, in the genome-reduced bacterium Mycoplasma pneumoniae. We envision FASTQINS and ANUBIS to aid in the analysis of Tn-seq procedures and lead to the development of accurate genome essentiality estimates to guide applications such as designing live vaccines or growth optimization.
  • dc.description.sponsorship ERASynBio 2nd Joint Call for Transnational Research Projects: ‘Building Synthetic Biology Capacity Through Innovative Translational Projects’, with funding from the corresponding ERASynBio National Funding Agencies; European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [670216] (MYCOCHASSIS); CERCA Programme/Generalitat de Catalunya; Spanish Ministry of Science and Innovation to the EMBL partnership, ‘Centro de Excelencia Severo Ochoa 2013–2017’. Funding for open access charge: ERASynBio 2nd Joint Call for Transnational Research Projects: ‘Building Synthetic Biology Capacity Through Innovative Translational Projects’, with funding from the corresponding ERASynBio National Funding Agencies; European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [670216] (MYCOCHASSIS); CERCA Programme/Generalitat de Catalunya; Spanish Ministry of Science and Innovation to the EMBL partnership, ‘Centro de Excelencia Severo Ochoa 2013–2017’.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Miravet-Verde S, Burgos R, Delgado J, Lluch-Senar M, Serrano L. FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies. Nucleic Acids Res. 2020; 48(17):e102. DOI: 10.1093/nar/gkaa679
  • dc.identifier.doi http://dx.doi.org/10.1093/nar/gkaa679
  • dc.identifier.issn 0305-1048
  • dc.identifier.uri http://hdl.handle.net/10230/45614
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Nucleic Acids Res. 2020; 48(17):e102
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/670216
  • dc.rights © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
  • dc.title FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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