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Review
. 2021 Sep 29;37(18):3021-3022.
doi: 10.1093/bioinformatics/btab101.

OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data

Sung-Joon Park  1 , Kenta Nakai  1
Affiliations
Review

OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data

Sung-Joon Park et al. Bioinformatics. .

Abstract

Summary: Microorganisms infect and contaminate eukaryotic cells during the course of biological experiments. Because microbes influence host cell biology and may therefore lead to erroneous conclusions, a computational platform that facilitates decontamination is indispensable. Recent studies show that next-generation sequencing (NGS) data can be used to identify the presence of exogenous microbial species. Previously, we proposed an algorithm to improve detection of microbes in NGS data. Here, we developed an online application, OpenContami, which allows researchers easy access to the algorithm via interactive web-based interfaces. We have designed the application by incorporating a database comprising analytical results from a large-scale public dataset and data uploaded by users. The database serves as a reference for assessing user data and provides a list of genera detected from negative blank controls as a 'blacklist', which is useful for studying human infectious diseases. OpenContami offers a comprehensive overview of exogenous species in NGS datasets; as such, it will increase our understanding of the impact of microbial contamination on biological and pathological traits.

Availability and implementation: OpenContami is freely available at: https://openlooper.hgc.jp/opencontami/.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Schematic overview of the OpenContami pipeline. (A) Users need to upload and submit a BAM file via OpenLooper GUIs. (B) The pipeline conducts rigorous read mapping and statistical testing of 11 365 microbe genomes. The results are used to build the OpenContami DB. GUI, graphical user interface; DB, database; RPMH, Reads Per Million Host-mapped reads; RPMU, Reads per Million host-Unmapped reads
See this image and copyright information in PMC

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References

    1. Consortium E.P. et al. (2020) Perspectives on ENCODE. Nature, 583, 693–698. - PMC - PubMed
    1. Genomes Project C. et al. (2015) A global reference for human genetic variation. Nature, 526, 68–74. - PMC - PubMed
    1. Ghandi M. et al. (2019) Next-generation characterization of the cancer cell line Encyclopedia. Nature, 569, 503–508. - PMC - PubMed
    1. Kumata R. et al. (2020) A tissue level atlas of the healthy human virome. BMC Biol., 18, 55. - PMC - PubMed
    1. Lappalainen T. et al.; The Geuvadis Consortium. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature, 501, 506–511. - PMC - PubMed

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