A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies

Inclusion and investigation of technical controls in microbiome sequencing studies is important for understanding technical biases and errors. Here, we present chkMocks, a general R-based tool that allows researchers to compare the composition of mock communities that are processed along with sample...

Descripción completa

Detalles Bibliográficos
Autores principales: Shetty, Sudarshan A., Kool, Jolanda, Fuentes, Susana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: OAE Publishing Inc. 2023
Materias:
Technical Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688813/
https://www.ncbi.nlm.nih.gov/pubmed/38047277
http://dx.doi.org/10.20517/mrr.2022.18
_version_ 1785152244132347904
author Shetty, Sudarshan A.
Kool, Jolanda
Fuentes, Susana
author_facet Shetty, Sudarshan A.
Kool, Jolanda
Fuentes, Susana
author_sort Shetty, Sudarshan A.
collection PubMed
description Inclusion and investigation of technical controls in microbiome sequencing studies is important for understanding technical biases and errors. Here, we present chkMocks, a general R-based tool that allows researchers to compare the composition of mock communities that are processed along with samples to their theoretical composition. A visual comparison between experimental and theoretical community composition and their correlation is provided for researchers to assess the quality of their sample processing workflows.
format Online
Article
Text
id pubmed-10688813
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher OAE Publishing Inc.
record_format MEDLINE/PubMed
spelling pubmed-106888132023-12-02 A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies Shetty, Sudarshan A. Kool, Jolanda Fuentes, Susana Microbiome Res Rep Technical Note Inclusion and investigation of technical controls in microbiome sequencing studies is important for understanding technical biases and errors. Here, we present chkMocks, a general R-based tool that allows researchers to compare the composition of mock communities that are processed along with samples to their theoretical composition. A visual comparison between experimental and theoretical community composition and their correlation is provided for researchers to assess the quality of their sample processing workflows. OAE Publishing Inc. 2023-04-27 /pmc/articles/PMC10688813/ /pubmed/38047277 http://dx.doi.org/10.20517/mrr.2022.18 Text en © The Author(s) 2023. https://creativecommons.org/licenses/by/4.0/© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing, adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Technical Note
Shetty, Sudarshan A.
Kool, Jolanda
Fuentes, Susana
A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies
title A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies
title_full A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies
title_fullStr A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies
title_full_unstemmed A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies
title_short A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies
title_sort tool to assess the mock community samples in 16s rrna gene-based microbiota profiling studies
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688813/
https://www.ncbi.nlm.nih.gov/pubmed/38047277
http://dx.doi.org/10.20517/mrr.2022.18
work_keys_str_mv AT shettysudarshana atooltoassessthemockcommunitysamplesin16srrnagenebasedmicrobiotaprofilingstudies
AT kooljolanda atooltoassessthemockcommunitysamplesin16srrnagenebasedmicrobiotaprofilingstudies
AT fuentessusana atooltoassessthemockcommunitysamplesin16srrnagenebasedmicrobiotaprofilingstudies
AT shettysudarshana tooltoassessthemockcommunitysamplesin16srrnagenebasedmicrobiotaprofilingstudies
AT kooljolanda tooltoassessthemockcommunitysamplesin16srrnagenebasedmicrobiotaprofilingstudies
AT fuentessusana tooltoassessthemockcommunitysamplesin16srrnagenebasedmicrobiotaprofilingstudies

Ejemplares similares