Persistent Gaps and Errors in Reference Databases Impede Ecologically Meaningful Taxonomy Assignments in 18S rRNA Studies: A Case Study of Terrestrial and Marine Nematodes [PDF]
Environmental DNAIn metabarcoding studies, Linnaean taxonomy assignments of Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs) underpin many downstream bioinformatics analyses and ecological interpretations of environmental DNA (eDNA) datasets ...
Alejandro De Santiago +6 more
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taxalogue: a toolkit to create comprehensive CO1 reference databases [PDF]
PeerJ, 2023 Background Taxonomic identification through DNA barcodes gained considerable traction through the invention of next-generation sequencing and DNA metabarcoding.
Niklas W. Noll +2 more
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Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies [PDF]
PeerJ, 2023 Background In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid ...
Francesco Mugnai +5 more
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The use of taxon-specific reference databases compromises metagenomic classification [PDF]
BMC Genomics, 2020 A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the ...
Vanessa R. Marcelino +2 more
doaj +2 more sources
Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling [PDF]
Frontiers in Microbiology, 2022 Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity.
Christina Karmisholt Overgaard +7 more
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A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data [PDF]
BMC Genomic Data, 2022 Background The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics ...
Benjamin Dubois +7 more
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Wide reference databases for typing Trypanosoma cruzi based on amplicon sequencing of the minicircle hypervariable region. [PDF]
PLoS Neglected Tropical Diseases, 2023 BackgroundTrypanosoma cruzi, the etiological agent of Chagas Disease, exhibits remarkable genetic diversity and is classified into different Discrete Typing Units (DTUs). Strain typing techniques are crucial for studying T. cruzi, because their DTUs have
Fanny Rusman +6 more
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Development of NIST Atomic Databases and Online Tools
Atoms, 2020 Over the last 25 years, the atomic standard reference databases and online tools developed at the National Institute of Standards and Technology (NIST) have provided users around the world with the highest-quality data on various atomic parameters (e.g.,
Yuri Ralchenko, Alexander Kramida
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Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax) [PDF]
mBio, 2020 High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental ...
Morten Simonsen Dueholm +7 more
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16S rRNA metabarcoding applied to the microbiome of insect products (novel food): a comparative analysis of three reference databases [PDF]
Italian Journal of Food SafetyThe 16S rRNA metabarcoding, based on Next-Generation Sequencing (NGS), is used to assess microbial biodiversity in various matrices, including food.
Gabriele Spatola +6 more
doaj +2 more sources