metaXplor: an interactive viral and microbial metagenomic data manager

Abstract Background 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 e...

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Veröffentlicht in:Gigascience Jg. 10; H. 2; S. 1 - 8
Hauptverfasser: Sempéré, Guilhem, Pétel, Adrien, Abbé, Magsen, Lefeuvre, Pierre, Roumagnac, Philippe, Mahé, Frédéric, Baurens, Gaël, Filloux, Denis
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States Oxford University Press 01.02.2021
Oxford Univ Press
Schlagworte:
Archives & records
Browsing
Cloud computing
Computers
Constraint modelling
Data search
Data visualization
Datasets
DNA barcoding
Laboratories
Life Sciences
Metadata
Metagenomics
Microorganisms
Personal computers
Phylogenetics
Phylogeny
Scientific visualization
Taxonomy
Technical Note
shotgun
sequence
metabarcoding
NoSQL
data management
web
metagenomics
assignment
taxonomy
sample
ISSN:2047-217X, 2047-217X
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Zusammenfassung:Abstract Background 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. Results 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. Conclusion 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.
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ISSN:2047-217X
2047-217X
DOI:10.1093/gigascience/giab001