Comparison of bioinformatic pipelines for eDNA metabarcoding data analysis of fish populations

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F25%3A00647068" target="_blank" >RIV/60077344:_____/25:00647068 - isvavai.cz</a>
Alternative codes found
RIV/60076658:12310/25:43909893
Result on the web
<a href="https://doi.org/10.3390/fishes10050214" target="_blank" >https://doi.org/10.3390/fishes10050214</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3390/fishes10050214" target="_blank" >10.3390/fishes10050214</a>

Result language
angličtina
Original language name
Comparison of bioinformatic pipelines for eDNA metabarcoding data analysis of fish populations
Original language description
Environmental DNA (eDNA) metabarcoding has gained popularity as a biomonitoring tool, leading to the emergence of various bioinformatic pipelines. However, comparisons are essential to assessing the reliability and similarity of results. In this study, we compared five bioinformatic pipelines (Anacapa, Barque, metaBEAT, MiFish, and SEQme) using samples collected from three reservoirs in the Czech Republic during the autumn and summer seasons. Negative and positive controls were used to monitor potential contamination during sample processing. eDNA was amplified, targeting the 12S fish rRNA gene, sequenced, and analyzed with the selected bioinformatic pipelines. Statistical analyses were applied to assess result similarity, including the number of detected taxa, read count, alpha and beta diversities, and the Mantel test. Our findings showed consistent taxa detection across pipelines, with increased sensitivity compared to traditional methods. Alpha and beta diversities and the Mantel test also exhibited significant similarities between pipelines. Divergences were observed based on the reservoir, season, and their interaction. In conclusion, the choice of bioinformatic pipeline did not significantly affect metabarcoding outcomes or their ecological interpretation.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project
<a href="/en/project/QK1920011" target="_blank" >QK1920011: Methodology of predatory fish quantification in drinking-water reservoirs to optimize the management of aquatic ecosystems</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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