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PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.019openalex-snapshot
Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity
inferredcites →https://doi.org/10.1016/j.funeco.2019.03.005openalex-snapshot
Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline
inferredcites →https://doi.org/10.1038/ismej.2017.119openalex-snapshot
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
inferredcites →https://doi.org/10.1038/nbt.3601openalex-snapshot
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
inferredcites →https://doi.org/10.1038/ncomms14087openalex-snapshot
Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity
inferredcites →https://doi.org/10.1038/s41587-019-0209-9openalex-snapshot
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
inferredcites →https://doi.org/10.1038/sdata.2017.27openalex-snapshot
Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btl529openalex-snapshot
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/btq725openalex-snapshot
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu595openalex-snapshot
BigDataScript: a scripting language for data pipelines
inferredcites →https://doi.org/10.1093/bioinformatics/bty767openalex-snapshot
Methods for automatic reference trees and multilevel phylogenetic placement
inferredcites →https://doi.org/10.1093/bioinformatics/btz305openalex-snapshot
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
inferredcites →https://doi.org/10.1093/gigascience/giaa022openalex-snapshot
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
inferredcites →https://doi.org/10.1093/gigascience/giz029openalex-snapshot
An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies
inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1093/nar/gky1022openalex-snapshot
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
inferredcites →https://doi.org/10.1093/nar/gky1078openalex-snapshot
The European Nucleotide Archive in 2018
inferredcites →https://doi.org/10.1093/sysbio/syy054openalex-snapshot
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
inferredcites →https://doi.org/10.1111/1755-0998.12428openalex-snapshot
obitools : a unix ‐inspired software package for DNA metabarcoding
inferredcites →https://doi.org/10.1111/1755-0998.12760openalex-snapshot
A fungal mock community control for amplicon sequencing experiments
inferredcites →https://doi.org/10.1111/1755-0998.12888openalex-snapshot
Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples
inferredcites →https://doi.org/10.1111/2041-210x.12399openalex-snapshot
PIPITS : an automated pipeline for analyses of fungal internal transcribed spacer sequences from the I llumina sequencing platform
inferredcites →https://doi.org/10.1111/ele.12162openalex-snapshot
Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05550.xopenalex-snapshot
Bioinformatic challenges for DNA metabarcoding of plants and animals
inferredcites →https://doi.org/10.1111/j.1471-8286.2007.01678.xopenalex-snapshot
bold : The Barcode of Life Data System (http://www.barcodinglife.org)
inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/aem.01630-16openalex-snapshot
Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities
inferredcites →https://doi.org/10.1128/msphere.00148-18openalex-snapshot
Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-13-31openalex-snapshot
PANDAseq: paired-end assembler for illumina sequences
inferredcites →https://doi.org/10.1186/1471-2164-14-s1-s7openalex-snapshot
BayesHammer: Bayesian clustering for error correction in single-cell sequencing
inferredcites →https://doi.org/10.1186/2049-2618-2-30openalex-snapshot
LotuS: an efficient and user-friendly OTU processing pipeline
inferredcites →https://doi.org/10.1371/journal.pone.0049334openalex-snapshot
CREST – Classification Resources for Environmental Sequence Tags
inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
inferredcites →https://doi.org/10.1371/journal.pone.0177459openalex-snapshot
Singularity: Scientific containers for mobility of compute
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.7287/peerj.preprints.27295v1openalex-snapshot
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
inferredcites →https://doi.org/10.7287/peerj.preprints.27295v2openalex-snapshot
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
inferredcites →https://doi.org/10.7717/peerj.1420openalex-snapshot
Swarm v2: highly-scalable and high-resolution amplicon clustering
inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot
VSEARCH: a versatile open source tool for metagenomics
inferredcites →https://doi.org/10.7717/peerj.3687openalex-snapshot
Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept
inferredcites →https://doi.org/10.7717/peerj.593openalex-snapshot
Swarm: robust and fast clustering method for amplicon-based studies
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.3897/bdj.13.e148981zenodo-depositor-declared
A long-term ecological research dataset from the marine genetic monitoring programme ARMS-MBON 2020-2021
inferred← citeshttps://doi.org/10.3897/bdj.14.e187301zenodo-depositor-declared
Microbial communities associated with two populations of the sponge Chondrilla nucula under present and projected climate conditions in the Aegean Sea
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inferred← citeshttps://doi.org/10.1002/edn3.255openalex-snapshot
Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies
inferred← citeshttps://doi.org/10.1002/edn3.382openalex-snapshot
General principles for assignments of communities from eDNA : Open versus closed taxonomic databases
inferred← citeshttps://doi.org/10.1002/wat2.1749openalex-snapshot
A new flow path: eDNA connecting hydrology and biology
inferred← citeshttps://doi.org/10.1007/698_2021_839openalex-snapshot
Seascape of Soft Bottom Benthic Communities in the Aegean Sea
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PIMBA: A PIpeline for MetaBarcoding Analysis
inferred← citeshttps://doi.org/10.1007/978-3-031-07055-6_13openalex-snapshot
Environmental DNA for Biodiversity Monitoring of Coral Reefs
inferred← citeshttps://doi.org/10.1007/s12526-024-01432-wopenalex-snapshot
Inventorizing marine biodiversity using eDNA data from Indonesian coral reefs: comparative high throughput analysis using different bioinformatic pipelines
inferred← citeshttps://doi.org/10.1016/b978-0-12-822861-6.00020-0openalex-snapshot
Phytoplankton diversity and ecology through the lens of high throughput sequencing technologies
inferred← citeshttps://doi.org/10.1016/j.aquaculture.2023.739249openalex-snapshot
Investigation of systemic granulomatosis in cultured meagre, Argyrosomus regius, using clinical metagenomics
inferred← citeshttps://doi.org/10.1016/j.copbio.2023.102936openalex-snapshot
Decoding dissolved information: environmental DNA sequencing at global scale to monitor a changing ocean
inferred← citeshttps://doi.org/10.1016/j.csbj.2023.01.034openalex-snapshot
VTAM: A robust pipeline for validating metabarcoding data using controls
inferred← citeshttps://doi.org/10.1016/j.csbj.2024.04.060openalex-snapshot
Visualizing metagenomic and metatranscriptomic data: A comprehensive review
inferred← citeshttps://doi.org/10.1016/j.ecolind.2025.113441openalex-snapshot
A systematic review on environmental DNA (eDNA) Science: An eco-friendly survey method for conservation and restoration of fragile ecosystems
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Use of metagenomics for the detection of pathogens in the environment: A scoping review
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Automating Microbial Community Analysis (AMCA): Development and application of an amplicon based graphical pipeline in patients with Chronic Kidney Disease
inferred← citeshttps://doi.org/10.1016/j.jia.2025.07.014openalex-snapshot
Monitoring agricultural arthropod diversity by eDNA metabarcoding from plant cleaning fluid
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Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization
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eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects
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Methodology for fish biodiversity monitoring with environmental DNA metabarcoding: The primers, databases and bioinformatic pipelines
inferred← citeshttps://doi.org/10.1080/02648725.2023.2197717openalex-snapshot
Unveiling the role of emerging metagenomics for the examination of hypersaline environments
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Metabarcoding for plant pathologists
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Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community
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Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology
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0s and 1s in marine molecular research: a regional HPC perspective
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Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake
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Dealing with the promise of metabarcoding in mega-event biomonitoring: EXPO2015 unedited data
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A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses
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A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS ‐ MBON 2018–2020
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A review of autonomous reef monitoring structures ( ARMS ) for monitoring hard‐bottom benthic biodiversity
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Best practices in metabarcoding of fungi: From experimental design to results
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CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
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Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility
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The gut microbiota intervenes in glucose tolerance and inflammation by regulating the biosynthesis of taurodeoxycholic acid and carnosine
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Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results
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A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)
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Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field
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An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies
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