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EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

Sarah Hunter, Matthew Corbett, Hubert Denise, Matthew Fraser, Alejandra Gonzalez-Beltran, Christopher Hunter, Philip Jones, Rasko Leinonen, Craig McAnulla, Eamonn Maguire, John Maslen, Alex Mitchell (+11 others)
2013 Nucleic Acids Research  
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

Alex Mitchell, Francois Bucchini, Guy Cochrane, Hubert Denise, Petra ten Hoopen, Matthew Fraser, Sebastien Pesseat, Simon Potter, Maxim Scheremetjew, Peter Sterk, Robert D. Finn
2015 Nucleic Acids Research  
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

Guy Cochrane, Rob Finn, Nils Peder Willassen, Lars Ailo Bongo, Monica Santamaria, Bruno Fosso, Eric Pelletier, Erwan Corre, Alex Mitchell, Simon Potter
2018 Zenodo  
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

Eric Pelletier, Erwan Corre, Guita Niang, Arnaud Meng, Mark Hoebeke, Robert Finn
2019 Zenodo  
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

Adibah Parmen, MOHD NOOR MAT ISA, FARAH FADWA BENBELGACEM, Hamzah Mohd Salleh, Ibrahim Ali Noorbatcha
2019 International Islamic University Malaysia Engineering Journal  
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

C. I. Hunter, A. Mitchell, P. Jones, C. McAnulla, S. Pesseat, M. Scheremetjew, S. Hunter
2012 Briefings in Bioinformatics  
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

Charles E Cook, Mary T Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney
2017 Nucleic Acids Research  
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

Pravin Dudhagara, Sunil Bhavsar, Chintan Bhagat, Anjana Ghelani, Shreyas Bhatt, Rajesh Patel
2015 Genomics, Proteomics & Bioinformatics  
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

Alex Mitchell, Maxim Scheremetjew, Gianluca De Moro, Bruno Fosso, Monica Santamaria, Graziano Pesole, Shriya Raj, Lars Ailo Bongo, Nils Peder Willassen, Robert D. Finn
2019 Zenodo  
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

Young M. Park, Silvano Squizzato, Nicola Buso, Tamer Gur, Rodrigo Lopez
2017 Nucleic Acids Research  
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

Igor B. Zhulin, W. W. Margolin
2015 Journal of Bacteriology  
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

Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen
2017 F1000Research  
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

Victor M Markowitz
2007 Current Opinion in Biotechnology  
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

Robert Finn, Alex Mitchell, Guy Cochrane, Josephine Burgin, Nils Peder Willassen
2019 Zenodo  
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  
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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