Codi de projecte: AGL 2015-73273-JIN
Paraules clau: Wine Qiime Pcr Next-generation-sequencing Metataxonomics Ion torrent Illumina Diversity Bioinformatics qiime pcr next-generation-sequencing metataxonomics ion torrent illumina bioinformatics
Data d'alta del registre: 2024-06-22
Versió de l'article dipositat: info:eu-repo/semantics/publishedVersion
URL Document de llicència: http://repositori.urv.cat/ca/proteccio-de-dades/
Referència a l'article segons font original: Frontiers In Microbiology. 10 (MAY): 1084-
Referència de l'ítem segons les normes 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
Acrònim: MetaConVin
Tipus de publicació: Journal Publications
Autor segons l'article: Kioroglou, Dimitrios; Mas, Albert; del Carmen Portillo, Maria
Departament: Bioquímica i Biotecnologia
Autor/s de la URV: Kioroglou, Dimitrios / Mas Baron, Alberto / Portillo Guisado, Maria del Carmen
Resum: 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.
Àrees temàtiques: 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
Accès a la llicència d'ús: https://creativecommons.org/licenses/by/3.0/es/
ISSN: 1664302X
Adreça de correu electrònic de l'autor: albert.mas@urv.cat carmen.portillo@urv.cat
Identificador de l'autor: 0000-0002-0763-1679 0000-0002-4576-0244
Data de publicació de l'article: 16 maig 2019
Enllaç font original: https://www.frontiersin.org/articles/10.3389/fmicb.2019.01084/full
Programa de finançament: Proyectos I+D+I para jóvenes investigadores sin vinculación o con vinculación temporal. Convocatoria 2015. Ministerio de Ciencia, Innovación y Universidades
DOI de l'article: 10.3389/fmicb.2019.01084
Entitat: Universitat Rovira i Virgili
Any de publicació de la revista: 2019
Acció del programa de finançament: Aplicación de Metagenómica y Metatranscriptómica al control microbiológico del vino de crianza
Repositori URV