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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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2019
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472834/ https://www.ncbi.nlm.nih.gov/pubmed/30958827 http://dx.doi.org/10.1371/journal.pcbi.1006967 |
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author | Martí, Jose Manuel |
author_facet | Martí, Jose Manuel |
author_sort | Martí, Jose Manuel |
collection | PubMed |
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 data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics. |
format | Online Article Text |
id | pubmed-6472834 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-64728342019-05-03 Recentrifuge: Robust comparative analysis and contamination removal for metagenomics Martí, Jose Manuel PLoS Comput Biol Research Article 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 data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics. Public Library of Science 2019-04-08 /pmc/articles/PMC6472834/ /pubmed/30958827 http://dx.doi.org/10.1371/journal.pcbi.1006967 Text en © 2019 Jose Manuel Martí http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Martí, Jose Manuel Recentrifuge: Robust comparative analysis and contamination removal for metagenomics |
title | 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_short | Recentrifuge: Robust comparative analysis and contamination removal for metagenomics |
title_sort | recentrifuge: robust comparative analysis and contamination removal for metagenomics |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472834/ https://www.ncbi.nlm.nih.gov/pubmed/30958827 http://dx.doi.org/10.1371/journal.pcbi.1006967 |
work_keys_str_mv | AT martijosemanuel recentrifugerobustcomparativeanalysisandcontaminationremovalformetagenomics |