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metaXplor: an interactive viral and microbial metagenomic data manager

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Zeitschriftentitel: GigaScience
Personen und Körperschaften: Sempéré, Guilhem, Pétel, Adrien, Abbé, Magsen, Lefeuvre, Pierre, Roumagnac, Philippe, Mahé, Frédéric, Baurens, Gaël, Filloux, Denis
In: GigaScience, 10, 2021, 2
Format: E-Article
Sprache: Englisch
veröffentlicht:
Oxford University Press (OUP)
Schlagwörter:
Computer Science Applications
Health Informatics
author_facet Sempéré, Guilhem
Pétel, Adrien
Abbé, Magsen
Lefeuvre, Pierre
Roumagnac, Philippe
Mahé, Frédéric
Baurens, Gaël
Filloux, Denis
Sempéré, Guilhem
Pétel, Adrien
Abbé, Magsen
Lefeuvre, Pierre
Roumagnac, Philippe
Mahé, Frédéric
Baurens, Gaël
Filloux, Denis
author Sempéré, Guilhem
Pétel, Adrien
Abbé, Magsen
Lefeuvre, Pierre
Roumagnac, Philippe
Mahé, Frédéric
Baurens, Gaël
Filloux, Denis
spellingShingle Sempéré, Guilhem
Pétel, Adrien
Abbé, Magsen
Lefeuvre, Pierre
Roumagnac, Philippe
Mahé, Frédéric
Baurens, Gaël
Filloux, Denis
GigaScience
metaXplor: an interactive viral and microbial metagenomic data manager
Computer Science Applications
Health Informatics
author_sort sempéré, guilhem
spelling Sempéré, Guilhem Pétel, Adrien Abbé, Magsen Lefeuvre, Pierre Roumagnac, Philippe Mahé, Frédéric Baurens, Gaël Filloux, Denis 2047-217X Oxford University Press (OUP) Computer Science Applications Health Informatics http://dx.doi.org/10.1093/gigascience/giab001 <jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.</jats:p></jats:sec> metaXplor: an interactive viral and microbial metagenomic data manager GigaScience
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title metaXplor: an interactive viral and microbial metagenomic data manager
title_unstemmed metaXplor: an interactive viral and microbial metagenomic data manager
title_full metaXplor: an interactive viral and microbial metagenomic data manager
title_fullStr metaXplor: an interactive viral and microbial metagenomic data manager
title_full_unstemmed metaXplor: an interactive viral and microbial metagenomic data manager
title_short metaXplor: an interactive viral and microbial metagenomic data manager
title_sort metaxplor: an interactive viral and microbial metagenomic data manager
topic Computer Science Applications
Health Informatics
url http://dx.doi.org/10.1093/gigascience/giab001
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description <jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.</jats:p></jats:sec>
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author Sempéré, Guilhem, Pétel, Adrien, Abbé, Magsen, Lefeuvre, Pierre, Roumagnac, Philippe, Mahé, Frédéric, Baurens, Gaël, Filloux, Denis
author_facet Sempéré, Guilhem, Pétel, Adrien, Abbé, Magsen, Lefeuvre, Pierre, Roumagnac, Philippe, Mahé, Frédéric, Baurens, Gaël, Filloux, Denis, Sempéré, Guilhem, Pétel, Adrien, Abbé, Magsen, Lefeuvre, Pierre, Roumagnac, Philippe, Mahé, Frédéric, Baurens, Gaël, Filloux, Denis
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description <jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.</jats:p></jats:sec>
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spelling Sempéré, Guilhem Pétel, Adrien Abbé, Magsen Lefeuvre, Pierre Roumagnac, Philippe Mahé, Frédéric Baurens, Gaël Filloux, Denis 2047-217X Oxford University Press (OUP) Computer Science Applications Health Informatics http://dx.doi.org/10.1093/gigascience/giab001 <jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.</jats:p></jats:sec> metaXplor: an interactive viral and microbial metagenomic data manager GigaScience
spellingShingle Sempéré, Guilhem, Pétel, Adrien, Abbé, Magsen, Lefeuvre, Pierre, Roumagnac, Philippe, Mahé, Frédéric, Baurens, Gaël, Filloux, Denis, GigaScience, metaXplor: an interactive viral and microbial metagenomic data manager, Computer Science Applications, Health Informatics
title metaXplor: an interactive viral and microbial metagenomic data manager
title_full metaXplor: an interactive viral and microbial metagenomic data manager
title_fullStr metaXplor: an interactive viral and microbial metagenomic data manager
title_full_unstemmed metaXplor: an interactive viral and microbial metagenomic data manager
title_short metaXplor: an interactive viral and microbial metagenomic data manager
title_sort metaxplor: an interactive viral and microbial metagenomic data manager
title_unstemmed metaXplor: an interactive viral and microbial metagenomic data manager
topic Computer Science Applications, Health Informatics
url http://dx.doi.org/10.1093/gigascience/giab001