ArticleGigaScience2020
Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed.
- Tree type-specific endophytic bacterial assembly and function in senescing leaves and needles in temperate forests of Central Europe.BMC plant biology · 2026Article
- Plant diversity influences plant volatile emission with varying effects at the species and community levels.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Plant and soil biodiversity sustain root mycorrhizal fungal richness under drought stress.The ISME journal · 2026Article
- Landscape effects on global soil pathogenic fungal diversity across spatial scales.Nature communications · 2026Article
- Complexity of leaf surface texture affects microbial colonization in temperate forest tree species.PloS one · 2026Article
- Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community.Frontiers in microbiology · 2026Article
- Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco.Genome biology · 2025Article
- Responses of maize roots, rhizosphere enzyme kinetics and prokaryote diversity to alternating precipitation: insights from a three-year field study.Annals of botany · 2025Article
- Long-Term Drought Persistently Shifts Plant and Soil Microbial Communities but Has Limited Impact on COGlobal change biology · 2025Article
- Uncovering the Role of Land Use Intensity in Shaping Forest and Grassland-Specific Soil Fungal Communities.Environmental microbiology · 2025Article
- Dynamics of zoosporic parasites in summer phytoplankton communities of the Baltic Sea.FEMS microbiology ecology · 2025Article
- Integrated multi-omics of feces, plasma and urine can describe and differentiate pediatric active Crohn's Disease from remission.Communications medicine · 2025Article
- Severe drought impacts tree traits and associated soil microbial communities of clonal oaks.Environmental microbiome · 2025Article
- Illuminating ecology and distribution of the rare fungus Phellinidium pouzarii in the Bavarian Forest National Park.Scientific reports · 2025Article
- Bark beetle infestation alters mycobiomes in wood, litter, and soil associated with Norway spruce.FEMS microbiology ecology · 2025Article
- Invertebrate Decline Has Minimal Effects on Oak-Associated Microbiomes.Environmental microbiology · 2025Article
- Functional diversity of soil macrofauna may contribute to microbial community stabilization under drought stress.Frontiers in microbiology · 2025Article
- Soil microbial communities are more disrupted by extreme drought than by gradual climate shifts under different land-use intensities.Frontiers in microbiology · 2025Article
- AmpWrap: a one-line fully automated amplicon metabarcoding 16S and 18S rRNA gene analysis.Bioinformatics advances · 2025Article
- Analysis of microbiome high-dimensional experimental design data using generalized linear models and ANOVA simultaneous component analysis.Frontiers in microbiomes · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAmplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.
resultsWe present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.
conclusionsBy use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.