MGnify: the microbiome analysis resource in 2020.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2020
08 01 2020
Historique:
accepted:
23
10
2019
received:
30
09
2019
pubmed:
7
11
2019
medline:
20
5
2020
entrez:
8
11
2019
Statut:
ppublish
Résumé
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 particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.
Identifiants
pubmed: 31696235
pii: 5614179
doi: 10.1093/nar/gkz1035
pmc: PMC7145632
doi:
Substances chimiques
DNA, Ribosomal Spacer
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D570-D578Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M011755/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R015228/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N018354/1
Pays : United Kingdom
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
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