ArticleBiologia futura2023
mkLTG: a command-line tool for taxonomic assignment of metabarcoding sequences using variable identity thresholds.
Article in Biologia futura, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Spatio-temporal metabarcoding surveys in ports reveal homogenised communities of non-indigenous species with high genetic diversity and connectivity.Scientific reports · 2026Article
- Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.Molecular ecology resources · 2026Article
- Characterization of the OmnivorousEcology and evolution · 2026Article
- Metabarcoding identifies macroalgal composition as a driver of benthic invertebrate assemblages in restored habitats.Scientific reports · 2025Article
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Authors and funding
1 author.
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Abstract
Metabarcoding is now a widely used method for biodiversity studies. Taxonomic assignment of environmental sequences is one of the key steps of metabarcoding. Assignments based on lowest common ancestor (LCA) method generally rely on fixed arbitrary thresholds, and this is generally not well adapted for assignment of taxonomically diverse groups with variable coverage in reference databases. The mkLTG is a LCA-based method that uses a series of percentage of identity thresholds starting from stringent parameters and decreasing it if necessary. All parameters can be set separately for each percentage of identity threshold, which makes this tool adaptable for different databases, genetic markers and diverse taxonomic groups. The optimization step was included using the COI marker and a comprehensive, non-redundant database. The mkLTG tool is a command-line application with few dependencies that runs in all operating systems, therefore, it is easy to include into complex pipelines. All scripts are freely available including the benchmarking at https://github.com/meglecz/mkLTG .
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