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Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
Wu, L.-Y.; Wijesekara, Y.; Piedade, G.; Pappas, N.; Brussaard, C.P.D.; Dutilh, B.E. (2024). Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes. Genome Biol. 25(1): 97. https://dx.doi.org/10.1186/s13059-024-03236-4
In: Genome Biology. BMC: London. ISSN 1465-6906; e-ISSN 1474-760X, more
Peer reviewed article  
Available in  Authors 
Authors  Top 
  • Wu, L.-Y.
  • Wijesekara, Y.
  • Piedade, G.
  • Pappas, N.
  • Brussaard, C.P.D., more
  • Dutilh, B.E.
Abstract

    Background

    As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.

    Results

    We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0–97%) and false positive rates (0–30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.

    Conclusions

    Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.

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