META-pipe cloud setup and execution

Agafonov, Aleksander; Mattila, Kimmo; Tuan, Cuong Duong; Tiede, Lars; Raknes, Inge Alexander; Bongo, Lars Ailo

doi:10.12688/f1000research.13204.3

Cited by 2 publications

(3 citation statements)

References 10 publications

(12 reference statements)

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“…As such, the Marine Metagenomics Community focused on metagenomics analysis pipelines, addressing the lack of reference databases and promoting the best practices for the research community. Highlights include the incorporation of new tools and resources into the MGnify 5 and MetaPIPE 6 analytical pipelines (e.g. MAPseq, ITSOneDB), 7,8 the formal description of the MGnify pipeline using the common workflow language (CWL 9 ) to promote interoperability, the establishment of the Marine Metagenomics Portal and MAR databases, 10 and a community paper (beyond ELIXIR) promoting best practices advocating the use of community standards for contextual provenance and metadata at all stages of the research data life cycle.…”

Section: From Marine Metagenomics To a More Inclusive Communitymentioning

confidence: 99%

Establishing the ELIXIR Microbiome Community

Finn,

Balech,

Burgin

et al. 2024

F1000Res

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Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and solutions to computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine studies, but are broadly applicable to all other biomes. Thus, expanding this Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broad range of biomes and link expertise across ‘omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.

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Section: From Marine Metagenomics To a More Inclusive Communitymentioning

confidence: 99%

Establishing the ELIXIR Microbiome Community

Finn,

Balech,

Burgin

et al. 2024

F1000Res

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“…Metagenomics (and especially 16S metagenomics) tool suites such as QIIME and Mothur have quite well-established pipelines. And end-to-end online analysis portals such as MG-RAST ( https://www.mg-rast.org/), MGnify ( https://www.ebi.ac.uk/metagenomics/pipelines/2.0), MOCAT2 ( https://mocat.embl.de/), META-pipe 1 and others have also been around for some time, and are also user-friendly GUI options. In general, the discussion of existing methods could be expanded. Please describe in more detail how MetaDEGalaxy fits in this ecosystem.In the introduction: "Currently, there is one end-to-end existing metagenomics workflow offering, ASaiM": a.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

et al. 2019

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Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences. While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs. Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics. MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

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META-pipe cloud setup and execution

Cited by 2 publications

References 10 publications

Establishing the ELIXIR Microbiome Community

Establishing the ELIXIR Microbiome Community

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

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