Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.
Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens aris...
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ftdoajarticles:oai:doaj.org/article:ced17f2d740448539b0fdd58f426eb97 2023-05-15T13:49:31+02:00 Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. Jose Manuel Martí 2019-04-01T00:00:00Z https://doi.org/10.1371/journal.pcbi.1006967 https://doaj.org/article/ced17f2d740448539b0fdd58f426eb97 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC6472834?pdf=render https://doaj.org/toc/1553-734X https://doaj.org/toc/1553-7358 1553-734X 1553-7358 doi:10.1371/journal.pcbi.1006967 https://doaj.org/article/ced17f2d740448539b0fdd58f426eb97 PLoS Computational Biology, Vol 15, Iss 4, p e1006967 (2019) Biology (General) QH301-705.5 article 2019 ftdoajarticles https://doi.org/10.1371/journal.pcbi.1006967 2022-12-31T11:42:27Z Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The ... Article in Journal/Newspaper Antarc* Antarctic Arctic Directory of Open Access Journals: DOAJ Articles Arctic Antarctic PLOS Computational Biology 15 4 e1006967 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
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Biology (General) QH301-705.5 |
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Biology (General) QH301-705.5 Jose Manuel Martí Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. |
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Biology (General) QH301-705.5 |
description |
Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The ... |
format |
Article in Journal/Newspaper |
author |
Jose Manuel Martí |
author_facet |
Jose Manuel Martí |
author_sort |
Jose Manuel Martí |
title |
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. |
title_short |
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. |
title_full |
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. |
title_fullStr |
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. |
title_full_unstemmed |
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. |
title_sort |
recentrifuge: robust comparative analysis and contamination removal for metagenomics. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2019 |
url |
https://doi.org/10.1371/journal.pcbi.1006967 https://doaj.org/article/ced17f2d740448539b0fdd58f426eb97 |
geographic |
Arctic Antarctic |
geographic_facet |
Arctic Antarctic |
genre |
Antarc* Antarctic Arctic |
genre_facet |
Antarc* Antarctic Arctic |
op_source |
PLoS Computational Biology, Vol 15, Iss 4, p e1006967 (2019) |
op_relation |
http://europepmc.org/articles/PMC6472834?pdf=render https://doaj.org/toc/1553-734X https://doaj.org/toc/1553-7358 1553-734X 1553-7358 doi:10.1371/journal.pcbi.1006967 https://doaj.org/article/ced17f2d740448539b0fdd58f426eb97 |
op_doi |
https://doi.org/10.1371/journal.pcbi.1006967 |
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PLOS Computational Biology |
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15 |
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4 |
container_start_page |
e1006967 |
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