2017
DOI: 10.1093/nar/gkx967
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EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

Abstract: EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignme… Show more

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Cited by 187 publications
(158 citation statements)
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References 44 publications
(45 reference statements)
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“…Both the UHGG and UHGP catalogues are available as part of a new genome layer within the MGnify 36 website, where summary statistics of each species cluster and their functional annotations can be interactively explored and downloaded (see ‘Data availability’ section for more details). We have also generated a BItsliced Genomic Signature Index (BIGSI) 37 of the UHGG, which will allow users to interactively screen for the presence of small sequence fragments (<5 kb) in this collection.…”
Section: Resultsmentioning
confidence: 99%
“…Both the UHGG and UHGP catalogues are available as part of a new genome layer within the MGnify 36 website, where summary statistics of each species cluster and their functional annotations can be interactively explored and downloaded (see ‘Data availability’ section for more details). We have also generated a BItsliced Genomic Signature Index (BIGSI) 37 of the UHGG, which will allow users to interactively screen for the presence of small sequence fragments (<5 kb) in this collection.…”
Section: Resultsmentioning
confidence: 99%
“…This approach is unable to provide the species and strain resolution generally required for detailed understanding of bacterial diversity [100]. With the wider adoption of metagenomic sequencing, standardised data reporting and more sophisticated bioinformatics tools alongside novel culture techniques, we should get a far better picture of the nature of sex differences in microbial communities [33, 100102]. …”
Section: Discussionmentioning
confidence: 99%
“…2.4.1 Quality control. MGnify version 4.1 (Mitchell et al, 2018) was used for merging paired end reads and quality control, which includes trimming, length filtering, and ambiguous base filtering by the SeqPrep (https://github.com/jstjohn/SeqPrep) and Trimmomatic (Bolger, Lohse, & Usadel, 2014) tools.…”
Section: Bioinformatics Analysesmentioning
confidence: 99%