ArticleBioinformatics (Oxford, England)2022
APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Using Metabarcoding Techniques to Map Multiple Dung Beetle-Vertebrate iDNA Networks in a Southeast Asian Forest.Molecular ecology resources · 2026Article
- Semi-Quantitative Monitoring of Plant-Arthropod Interactions by eDNA Metabarcoding of Individual Flowers and Leaves.Ecology and evolution · 2026Article
- Oxygen Minimum Zone and Organic Carbon Structure Benthic Prokaryotic Communities and Metabolism in Warm Deep-Red Sea Sediments.Microorganisms · 2026Article
- Testing newly developed PCR primers for high-specificity enrichment of bees from terrestrial eDNA.BMC research notes · 2026Article
- From fish to invertebrates: multi-marker eDNA metabarcoding for monitoring wetland biodiversity and non-indigenous species in Macao SAR China.Scientific reports · 2026Article
- Assessing Prokaryotic Benthic Communities in the Red Sea.Environmental microbiology · 2026Article
- Article
- Assessment of leaf-litter invertebrate biodiversity using high throughput sequencing.PloS one · 2026Article
- Cross-Platform Evaluation of Established NGS-Based Metabarcoding Methods for Detecting Food Fraud in Pistachio Products.Foods (Basel, Switzerland) · 2026Article
- Multiscale Patterns of Bacterial and Protist Diversity Across Red Sea Coral Reefs.Microorganisms · 2025Article
- Specific host-algae relationship, yet flexible bacterial microbiome, in diatom-bearing foraminifera.Science advances · 2025Article
- Authenticity in bakery products: Detection of pistachio fraud using NGS metabarcoding.Food chemistry. Molecular sciences · 2025Article
- Metacommunity Theory and Metabarcoding Reveal the Environmental, Spatial and Biotic Drivers of Meiofaunal Communities in Sandy Beaches.Molecular ecology · 2025Article
- Benthic Feeding and Diet Partitioning in Red Sea Mesopelagic Fish Resolved Through DNA Metabarcoding and ROV Footage.Ecology and evolution · 2025Article
- Intestinal dysbiosis in critically ill patients: a case-control study ofFrontiers in medicine · 2025Article
- Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.Molecular ecology resources · 2025Article
- AmpWrap: a one-line fully automated amplicon metabarcoding 16S and 18S rRNA gene analysis.Bioinformatics advances · 2025Article
- Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free.BMC genomics · 2024Article
- Unlocking rivers' hidden diversity and ecological status using DNA metabarcoding in Northwest Spain.Ecology and evolution · 2024Article
- A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.Molecular ecology resources · 2024Review
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3 authors.
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Abstract
summaryDNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide and consequently the number and size of data sets increases exponentially. To date, no published DNA metabarcoding data processing pipeline exists that is (i) platform independent, (ii) easy to use [incl. graphical user interface (GUI)], (iii) fast (does scale well with dataset size) and (iv) complies with data protection regulations of e.g. environmental agencies. The presented pipeline APSCALE meets these requirements and handles the most common tasks of sequence data processing, such as paired-end merging, primer trimming, quality filtering, clustering and denoising of any popular metabarcoding marker, such as internal transcribed spacer, 16S or cytochrome c oxidase subunit I. APSCALE comes in a command line and a GUI version. The latter provides the user with additional summary statistics options and links to GUI-based downstream applications. AVAILABILITY AND IMPLEMENTATION: APSCALE is written in Python, a platform-independent language, and integrates functions of the open-source tools, VSEARCH (Rognes et al., 2016), cutadapt (Martin, 2011) and LULU (Frøslev et al., 2017). All modules support multithreading to allow fast processing of larger DNA metabarcoding datasets. Further information and troubleshooting are provided on the respective GitHub pages for the command-line version (https://github.com/DominikBuchner/apscale) and the GUI-based version (https://github.com/TillMacher/apscale_gui), including a detailed tutorial. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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