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EBI metagenomics—a new resource for the analysis and archiving of metagenomic data
2013
Nucleic Acids Research
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Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. ...
In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/ metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic ...
ACKNOWLEDGEMENTS The authors would like to thank users from the metagenomics community who have volunteered in usability studies and/or provided feedback to us via surveys and emails; they are too numerous ...
doi:10.1093/nar/gkt961
pmid:24165880
pmcid:PMC3965009
fatcat:omjatsv6lrhklc5qhkldkhejl4
EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data
2015
Nucleic Acids Research
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EBI metagenomics (https://www.ebi.ac.uk/ metagenomics/) is a freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. ...
In particular, we describe updates to data content, a complete overhaul of the analysis pipeline, streamlining of data presentation via the website and the development of a new web based tool to compare ...
Rather than develop an entirely new repository for metagenomic data, EMG has partnered with the European Nucleotide Archive (ENA) (18) to provide a permanent metagenomics data archive and data sharing ...
doi:10.1093/nar/gkv1195
pmid:26582919
pmcid:PMC4702853
fatcat:llg5scj4lba7hndt673ldh3xhi
Elixir-Excelerate: Deliverable 6.2: Report On Comprehensive Metagenomic Data Standards Environment
2018
Zenodo
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Language (CWL) We describe that in response to our third recommendation - that the results of computational metabarcoding and metagenomics analysis processes be archived. ...
On our first recommendation - that scientists comply with data standards and recommended best practices, we assess in this Annex the status across sampling, sequencing, analysis and results archiving stages ...
("analysis"); and finally, data are archived and published ("archiving"). ...
doi:10.5281/zenodo.1229220
fatcat:evhtrnvuijavndvoi2xrxoyjv4
ELIXIR-EXCELERATE D6.5: Improvement and Application of Eukaryotic Gene catalogue
2019
Zenodo
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A new resource, METdb, has been established to house the data produced from the outputs of the assembly and annotation workflow runs on 489 transcriptomes. ...
This new resource dramatically increases the representation of micro-eukaryotic organisms, both in this new database, as well as being propagated to core data resources such as ENA and UniProtKB. ...
(Task 6.1) of databases specific for the marine metagenomics. (Task 6.2) Evaluation and implementation of tools and pipelines for metagenomics analysis. ...
doi:10.5281/zenodo.3234521
fatcat:hd3lxdjedjbldothtk5mz26wue
COMPARATIVE METAGENOMICS ANALYSIS OF PALM OIL MILL EFFLUENT (POME) USING THREE DIFFERENT BIOINFORMATICS PIPELINES
2019
International Islamic University Malaysia Engineering Journal
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RAST server (MG-RAST), Integrated Microbial Genomes with Microbiome Samples (IMG/M) and European Bioinformatics Institute (EBI) Metagenomics, in term of the taxonomic assignment and functional analysis ...
However, in term of analysis of results, IMG/M provides more variety of phylum with wider percent identities for taxonomical assignment and IMG/M provides the highest carbohydrates, amino acids, lipids ...
Besides that, the authors also deeply grateful to Malaysia Genome Institute (MGI) for the technical assistance in analyzing the metagenomic data of POME. ...
doi:10.31436/iiumej.v20i1.909
fatcat:q34yhciuhvd3ndvfptdxcmjs6u
Metagenomic analysis: the challenge of the data bonanza
2012
Briefings in Bioinformatics
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Hand-in-hand with this data bonanza comes the computationally overwhelming task of analysis. ...
Herein, we describe some of the bioinformatic approaches currently used by metagenomics researchers to analyze their data, the issues they face and the steps that could be taken to help overcome these ...
Acknowledgements The authors thank Penny Hirsch for helpful discussions about this manuscript. ...
doi:10.1093/bib/bbs020
pmid:22962339
pmcid:PMC3504930
fatcat:f36nozc5lzfwrdwitfljvx6rz4
The European Bioinformatics Institute in 2017: data coordination and integration
2017
Nucleic Acids Research
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Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. ...
This update gives a birds-eye view of EMBL-EBI's approach to data integration and service development as genomics begins to enter the clinic. ...
EBI Metagenomics (39) is a freely available hub for the archiving, analysis and exploration of metagenomic datasets. ...
doi:10.1093/nar/gkx1154
pmid:29186510
pmcid:PMC5753251
fatcat:ubzlegb2kjcltbtdftwsh6mlja
Web Resources for Metagenomics Studies
2015
Genomics, Proteomics & Bioinformatics
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In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. ...
The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. ...
Acknowledgments The authors are thankful to BIT Virtual Centre, Patan Node, Hemchandracharya North Gujarat University, India for providing servers and computational facilities. ...
doi:10.1016/j.gpb.2015.10.003
pmid:26602607
pmcid:PMC4678780
fatcat:uldztj42fbdqvbq55u3poyigeq
ELIXIR-EXCELERATE D6.3: Report describing a set of tools, pipelines and search engine for interrogation of marine metagenomic data
2019
Zenodo
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marine shotgun metagenomics datasets developed. ● Cloud deployment of pipelines to increase compute capacity. ● New data analysis outputs that will feed the databases developed as part of this work package ...
● Pipelines expanded to increase scope of analysis, tools updated and tailoring of analysis to meet the demands of the Marine Metagenomics community. ● Analysis pipelines described in the Common Workflow ...
We overcame the data transfer issues by developing a new component for data ingress using an FTP pull first, while the bulk transfer of results back to the EMBL-EBI filesystem was achieved via a direct ...
doi:10.5281/zenodo.3228301
fatcat:nb2r64odubauno62doau6n5lr4
The EBI search engine: EBI search as a service—making biological data accessible for all
2017
Nucleic Acids Research
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The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include ...
We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. ...
Portal and Peter Walter and Ken Hawkins for UX on the new GUI. ...
doi:10.1093/nar/gkx359
pmid:28472374
pmcid:PMC5570174
fatcat:7vlgpmowhrgcvjhqn2sk7w4hse
Databases for Microbiologists: TABLE 1
2015
Journal of Bacteriology
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The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists. ...
They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. ...
Work in my laboratory is supported by grants GM072285 and DE024463 from the National Institutes of Health. ...
doi:10.1128/jb.00330-15
pmid:26013493
pmcid:PMC4505447
fatcat:6eyuvuplzjc7ravlhhmk6isg6i
ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
2017
F1000Research
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Mitchell A, Bucchini F, Cochrane G, et al.: EBI metagenomics in 2016 --an expanding and evolving resource for the analysis and archiving of metagenomic data. ...
.: EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 2013; 42(Database issue): D600-6. PubMed Abstract | Publisher Full Text | Free Full Text 4. ...
Acknowledgements We would like to thank Concetta de Santi for isolating DNA from the environmental samples and Seila Pandur for running the MiSeq sequencer. Page 10 of 18 ...
doi:10.12688/f1000research.10443.1
pmid:28620454
pmcid:PMC5461914
fatcat:aie2ujmvtfaitkjnlgyjxdgvgm
Microbial genome data resources
2007
Current Opinion in Biotechnology
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Acknowledgements The work presented in this paper was supported by the Director, Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. ...
The report includes a chapter on metagenome data management and addresses the problem of funding for the collection, storage and analysis of the massive amounts of metagenome data expected to be generated ...
Microbial genomes can be explored using a variety of analysis tools provided by resources that often further enrich the data in archival or curated public resources. ...
doi:10.1016/j.copbio.2007.04.005
pmid:17467973
fatcat:xar5m3dtf5dmtglad2pe6l2nku
ELIXIR-EXCELERATE D6.4: Report on assessment criteria and standardisation of metagenome assembled genomes (MAGs) from Marine samples
2019
Zenodo
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Description of the new infrastructure in the European Nucleotide Archive, and how this has been structured to accommodate the data generated within WP6 (and more broadly). ...
Demonstration of the application of completeness/contamination estimates on metagenome assembled genomes (MAGs) produced as part of WP6. ...
Primary metagenome assemblies and binned metagenome assemblies are handled in a new data structure, specifically a class of the ENA Analysis object, that provides a simple metadata record with pointer ...
doi:10.5281/zenodo.3234519
fatcat:t4tznbnkbbagbcerepggw7g3e4
MGnify: the microbiome analysis resource in 2020
2019
Nucleic Acids Research
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MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in ...
Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. ...
MGnify (previously known as EBI Metagenomics ( 14 )) is a freely available hub for the analysis, exploration and archiving of microbiome data. ...
doi:10.1093/nar/gkz1035
pmid:31696235
pmcid:PMC7145632
fatcat:65fvxg66kvapdavttbvccrou2u
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