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: 2023-02-18

Papper version: info:eu-repo/semantics/publishedVersion

Licence document URL: http://repositori.urv.cat/ca/proteccio-de-dades/

Papper original source: Frontiers In Microbiology. 10 (MAY): 1084-

APA: Kioroglou D; Mas A; Del Carmen Portillo M (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

Acronym: MetaConVin

Publication Type: Journal Publications

Author, as appears in the article.: Kioroglou D; Mas A; Del Carmen Portillo M

Department: Bioquímica i Biotecnologia

URV's Author/s: Kioroglou, Dimitrios / Mas Baron, Alberto

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

Author identifier: 0000-0002-0763-1679

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