Research output: Contribution to journal › Article › peer-review
MGnify : the microbiome analysis resource in 2020. / Mitchell, Alex L.; Almeida, Alexandre; Beracochea, Martin; Boland, Miguel; Burgin, Josephine; Cochrane, Guy; Crusoe, Michael R.; Kale, Varsha; Potter, Simon C.; Richardson, Lorna J.; Sakharova, Ekaterina; Scheremetjew, Maxim; Korobeynikov, Anton; Shlemov, Alex; Kunyavskaya, Olga; Lapidus, Alla; Finn, Robert D.
In: Nucleic Acids Research, Vol. 48, No. D1, 01.01.2020, p. D570-D578.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - MGnify
T2 - the microbiome analysis resource in 2020
AU - Mitchell, Alex L.
AU - Almeida, Alexandre
AU - Beracochea, Martin
AU - Boland, Miguel
AU - Burgin, Josephine
AU - Cochrane, Guy
AU - Crusoe, Michael R.
AU - Kale, Varsha
AU - Potter, Simon C.
AU - Richardson, Lorna J.
AU - Sakharova, Ekaterina
AU - Scheremetjew, Maxim
AU - Korobeynikov, Anton
AU - Shlemov, Alex
AU - Kunyavskaya, Olga
AU - Lapidus, Alla
AU - Finn, Robert D.
N1 - Funding Information: European Union’s Horizon 2020 Research and Innovation programme [676559 and 817729]; Biotechnology and Biosciences Research Council [BB/M011755/1, BB/R015228/1 and BB/N018354/1]; ELIXIR, the research infrastructure for Life-science data; Russian Fund for Basic Research [18-54-74004]; European Molecular Biology Laboratory core funds. Funding for open access charge: Research Councils UK (RCUK). Conflict of interest statement. None declared.
PY - 2020/1/1
Y1 - 2020/1/1
N2 - 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.
AB - 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.
KW - Archaea/classification
KW - Bacteria/classification
KW - DNA, Ribosomal Spacer/genetics
KW - Databases, Genetic
KW - Metagenome
KW - Metagenomics/methods
KW - Microbiota
KW - Phylogeny
KW - Software
UR - http://www.scopus.com/inward/record.url?scp=85077668671&partnerID=8YFLogxK
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1035/5614179
UR - http://www.mendeley.com/research/mgnify-microbiome-analysis-resource-2020
U2 - 10.1093/nar/gkz1035
DO - 10.1093/nar/gkz1035
M3 - Article
C2 - 31696235
VL - 48
SP - D570-D578
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - D1
ER -
ID: 49579657