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Contamination detection in genomic data: more is not enough

The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools t...

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Detalles Bibliográficos
Autores principales: Cornet, Luc, Baurain, Denis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8862208/
https://www.ncbi.nlm.nih.gov/pubmed/35189924
http://dx.doi.org/10.1186/s13059-022-02619-9
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author Cornet, Luc
Baurain, Denis
author_facet Cornet, Luc
Baurain, Denis
author_sort Cornet, Luc
collection PubMed
description The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algorithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selection of appropriate tools for specific applications. Finally, we present future challenges in the developing field of contamination detection. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02619-9.
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spelling pubmed-88622082022-02-23 Contamination detection in genomic data: more is not enough Cornet, Luc Baurain, Denis Genome Biol Review The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algorithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selection of appropriate tools for specific applications. Finally, we present future challenges in the developing field of contamination detection. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02619-9. BioMed Central 2022-02-21 /pmc/articles/PMC8862208/ /pubmed/35189924 http://dx.doi.org/10.1186/s13059-022-02619-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Review
Cornet, Luc
Baurain, Denis
Contamination detection in genomic data: more is not enough
title Contamination detection in genomic data: more is not enough
title_full Contamination detection in genomic data: more is not enough
title_fullStr Contamination detection in genomic data: more is not enough
title_full_unstemmed Contamination detection in genomic data: more is not enough
title_short Contamination detection in genomic data: more is not enough
title_sort contamination detection in genomic data: more is not enough
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8862208/
https://www.ncbi.nlm.nih.gov/pubmed/35189924
http://dx.doi.org/10.1186/s13059-022-02619-9
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