“HAPP: High-accuracy pipeline for processing deep metabarcoding data” from Fredrik Ronquist’s group
doi.org/10.1371/jour... #metabarcodingHAPP: High-accuracy pipeline f...
HAPP: High-accuracy pipeline for processing deep metabarcoding data
Author summary Charting and monitoring biodiversity is essential for understanding and protecting ecosystems, but it has been difficult to collect data cost-efficiently at scale. An approach that potentially solves this problem is metabarcoding—a method that can be applied to DNA from environmental samples to identify many species at once. Unfortunately, it may produce misleading results due to noise in the data. A particularly challenging problem when analysing data from mitochondrial DNA, such as the CO1 gene often used for analysing insect biodiversity, is the existence of nuclear encoded copies of the gene that can severely inflate diversity estimates. We created an algorithm called NEEAT that helps remove such misleading signals by combining information from multiple samples and spotting unusual patterns of genetic change. We also tested many existing tools for other steps of data processing, and combined NEEAT with the best tools in creating a new, high-accuracy analysis pipeline we call HAPP. Using both simulated and real-world insect data, we show that our approach is not only more accurate than current methods but also efficient at handling large datasets. Our work aims to make biodiversity studies more precise and scalable, supporting better conservation and environmental decision-making.
Release Ampliseq release 2.16.1 2026-01-23 · nf-core/ampliseq
Two bug fixes plus modifications to adhere to Nextflow strict syntax.
Fixed
#943 - Fix SciLifeLab Figshare urls for reference databases.
#942 - Nextflow strict syntax for non-nf-core-modules/workf...
"The soil microbiome as an indicator of ecosystem multifunctionality in European soils"
TLDR - Reinforces the link between soil properties and microbes (bacteria and fungi) driving multiple ecosystem functions with integrated DNA metabarcoding and enzyme analysis approaches.
https://www.nature.com/articles/s41467-025-67353-9
#LUCAS #soil #metabarcoding #function #EnzymeActivity #IndicatorSpecies #monitoring
The soil microbiome as an indicator of ecosystem multifunctionality in European soils - Nature Communications
Soil microorganisms play a crucial role in maintaining ecosystem functioning across diverse environments. This study shows that soil properties and specific microbial taxa jointly shape ecosystem functioning across European soils.
Are we throwing away good data? Evaluation of chimera detection algorithms on long-read amplicons reveals high false-positive rates across algorithms
TLDR - uchime_denovo using default parameters offers the best precision and recall
https://peerj.com/articles/20456/
#DNA #metabarcoding #chimera #SimulationStudy
Are we throwing away good data? Evaluation of chimera detection algorithms on long-read amplicons reveals high false-positive rates across algorithms
Long-read amplicon sequencing has enabled us to return to full-length DNA barcodes, which benefit from the higher taxonomic resolution in metabarcoding-based biodiversity studies. However, chimeric sequences (artificial constructs formed when incomplete amplicons fuse during polymerase chain reaction (PCR)) remain challenging, potentially skewing diversity estimates and ecological inferences. Here, we benchmark three de novo chimera detection algorithms, uchime_denovo, removeBimeraDenovo, and chimeras_denovo, on simulated and empirical eukaryotic full-ITS (rRNA ITS1-5.8S-ITS2) datasets to evaluate their precision, sensitivity, and effects on the final OTUs composition/community structure. Upon simulated data, uchime_denovo achieved the highest precision even with default settings, whereas other algorithms displayed high false-positive chimera rates without setting adjustments. Similarly, the tests upon empirical data showed that uchime_denovo had lower false positive rates, whereas about half of the sequences in the putative chimeric batch were false positives when using chimeras_denovo and removeBimeraDenovo. We found that most of the false-negative chimeras contained multiple 5.8S regions, indicating PacBio library preparation artifacts rather than PCR artifacts. However, OTU-level comparisons indicated that overall richness and community-ordination patterns remain largely consistent across different chimera-filtering approaches with or without accounting for false positives and negatives.
Our new
@[email protected] paper on Advancing ecological
#assessment: towards the integration of
#eDNA #metabarcoding into an estuarine
#fish index is out.
#Research
#MarineEcology
#GES4SEAS
Free download here:
authors.elsevier.com/sd/article/S...Happy to share our new paper by Clarisse Lemonnier et al.:
Comparison of
#Metabarcoding and
#Shotgun Sequencing Confirms the Relevance of Chloroplastic rRNA Genes to Assess Community Structure of
#Lake #Phytoplanktonhttps://onlinelibrary.wiley.com/doi/10.1111/1755-0998.70077#metagenomics in Mol Ecol Res
Happy to share our new paper in ISME communications:
Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms
Kulaš, Lemmonnier, Alric, Kahlert, Trobajo, Udovič & Rimet
https://doi.org/10.1093/ismeco/ycaf171#biogeography #diatom #metabarcoding #rivers #biodiversity #species
Invasive species monitoring based on eDNA multiplex PCR sequencing
Invasive species pose a significant threat to global biodiversity and the stability of ecosystems. Although environmental DNA (eDNA)-based quantitative PCR is considered effective, its limited multiplexing capacity makes it impractical for large-scale monitoring of invasive species. To address this limitation, we developed a novel and efficient approach for invasive species monitoring by combining multiplex PCR amplification with high-throughput sequencing. In this study, we screened 46 aquatic invasive species of major concern in China. We have integrated and designed 91 pairs of primers that can simultaneously amplify these species in a single PCR system. The validated method was applied to field monitoring in the Pearl River Basin to evaluate its practical performance. Multiplex PCR sequencing successfully detected 28 invasive species, with over 90% of environmental samples testing positive for invasive species DNA, demonstrating the method’s high sensitivity and broad applicability. Furthermore, all 11 invasive species identified through metabarcoding were also consistently detected by multiplex PCR sequencing, showing a strong positive correlation and high concordance across all monitoring sites. In conclusion, multiplex PCR sequencing represents a powerful and cost-effective tool for simultaneously detecting multiple aquatic invasive species in the early stages of invasion. It significantly improves detection efficiency, reduces monitoring costs and provides a solid foundation for developing a scientific and scalable monitoring system for aquatic invasive species.
Rod Page
Teresita Porter 🙋🏻♀️
nf-core
Dr Angel Borja
Frédéric Rimet
