Articles producció científica> Bioquímica i Biotecnologia

Evaluating the effect of QIIME balanced default parameters on metataxonomic analysis workflows with a mock community

  • Identification data

    Identifier: imarina:5874111
    Authors:
    Kioroglou, DimitriosMas, Albertdel Carmen Portillo, Maria
    Abstract:
    Copyright © 2019 Kioroglou, Mas and Portillo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Metataxonomic analysis represents a fast and cost-effective approach for acquiring informative insight into the composition of the microbiome of samples with variable diversity, such as wine samples. Nevertheless, it comprises a vast amount of laboratory procedures and bioinformatic frameworks each one associated with an inherent variability of protocols and algorithms, respectively. As a solution to the bioinformatic maze, QIIME bioinformatic framework has incorporated benchmarked, and balanced parameters as default parameters. In the current study, metataxonomic analysis of two types of mock community standards with the same microbial composition has been performed for evaluating the effectivess of QIIME balanced default parameters on a variety of aspects related to different laboratory and bioinformatic workflows. These aspects concern NGS platforms, PCR protocols, bioinformatic pipelines, and taxonomic classification algorithms. Several qualitative performance expectations have been the outcome of the analysis, rendering the mock community a useful evaluation tool.
  • Others:

    Project code: AGL 2015-73273-JIN
    Keywords: Wine Qiime Pcr Next-generation-sequencing Metataxonomics Ion torrent Illumina Diversity Bioinformatics qiime pcr next-generation-sequencing metataxonomics ion torrent illumina bioinformatics
    Record's date: 2024-06-22
    Papper version: info:eu-repo/semantics/publishedVersion
    Papper original source: Frontiers In Microbiology. 10 (MAY): 1084-
    APA: Kioroglou, Dimitrios; Mas, Albert; del Carmen Portillo, Maria (2019). Evaluating the effect of QIIME balanced default parameters on metataxonomic analysis workflows with a mock community. Frontiers In Microbiology, 10(MAY), 1084-. DOI: 10.3389/fmicb.2019.01084
    Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
    Acronym: MetaConVin
    Publication Type: Journal Publications
    Author, as appears in the article.: Kioroglou, Dimitrios; Mas, Albert; del Carmen Portillo, Maria
    Department: Bioquímica i Biotecnologia
    URV's Author/s: Kioroglou, Dimitrios / Mas Baron, Alberto / Portillo Guisado, Maria del Carmen
    Abstract: Copyright © 2019 Kioroglou, Mas and Portillo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Metataxonomic analysis represents a fast and cost-effective approach for acquiring informative insight into the composition of the microbiome of samples with variable diversity, such as wine samples. Nevertheless, it comprises a vast amount of laboratory procedures and bioinformatic frameworks each one associated with an inherent variability of protocols and algorithms, respectively. As a solution to the bioinformatic maze, QIIME bioinformatic framework has incorporated benchmarked, and balanced parameters as default parameters. In the current study, metataxonomic analysis of two types of mock community standards with the same microbial composition has been performed for evaluating the effectivess of QIIME balanced default parameters on a variety of aspects related to different laboratory and bioinformatic workflows. These aspects concern NGS platforms, PCR protocols, bioinformatic pipelines, and taxonomic classification algorithms. Several qualitative performance expectations have been the outcome of the analysis, rendering the mock community a useful evaluation tool.
    Thematic Areas: Zootecnia / recursos pesqueiros Saúde coletiva Química Odontología Nutrição Microbiology (medical) Microbiology Medicina veterinaria Medicina ii Medicina i Materiais Matemática / probabilidade e estatística Interdisciplinar Geografía Geociências Farmacia Ensino Engenharias iii Engenharias ii Engenharias i Economia Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências ambientais Ciências agrárias i Ciência de alimentos Ciência da computação Biotecnología Biodiversidade Astronomia / física
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    ISSN: 1664302X
    Author's mail: albert.mas@urv.cat carmen.portillo@urv.cat
    Author identifier: 0000-0002-0763-1679 0000-0002-4576-0244
    Paper data publication: 16 maig 2019
    Link to the original source: https://www.frontiersin.org/articles/10.3389/fmicb.2019.01084/full
    Funding program: Proyectos I+D+I para jóvenes investigadores sin vinculación o con vinculación temporal. Convocatoria 2015. Ministerio de Ciencia, Innovación y Universidades
    Article's DOI: 10.3389/fmicb.2019.01084
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2019
    Funding program action: Aplicación de Metagenómica y Metatranscriptómica al control microbiológico del vino de crianza
  • Keywords:

    Microbiology,Microbiology (Medical)
    Wine
    Qiime
    Pcr
    Next-generation-sequencing
    Metataxonomics
    Ion torrent
    Illumina
    Diversity
    Bioinformatics
    qiime
    pcr
    next-generation-sequencing
    metataxonomics
    ion torrent
    illumina
    bioinformatics
    Zootecnia / recursos pesqueiros
    Saúde coletiva
    Química
    Odontología
    Nutrição
    Microbiology (medical)
    Microbiology
    Medicina veterinaria
    Medicina ii
    Medicina i
    Materiais
    Matemática / probabilidade e estatística
    Interdisciplinar
    Geografía
    Geociências
    Farmacia
    Ensino
    Engenharias iii
    Engenharias ii
    Engenharias i
    Economia
    Ciências biológicas iii
    Ciências biológicas ii
    Ciências biológicas i
    Ciências ambientais
    Ciências agrárias i
    Ciência de alimentos
    Ciência da computação
    Biotecnología
    Biodiversidade
    Astronomia / física
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