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bioRxiv · 10.1101/2025.08.27.672749

TIPP-SD: A New Method for Species Detection in Microbiomes

Shen, C.·Wedell, E.·Pop, M.·Warnow, T.
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Abstract

In this study, we present TIPP-SD (i.e., TIPP for Species Detection), a new technique for species detection in a microbiome sample. TIPP-SD uses a modified version of TIPP3, which is a recently developed abundance profiling tool based on maximum likelihood phylogenetic placement into marker gene taxonomies. TIPP-SD depends on a parameter (i.e., "thresh-old") for the required support for species detection, thus allowing us to compute a precision-recall curve as we vary this parameter. In comparing the precision-recall curves for TIPP-SD, TIPP3, Kraken2, Bracken, and Metapresence, we find that TIPP-SD improves on the other methods with respect to accuracy under conditions where some species occur in low abundance, or where there is sequencing error. Under easier conditions, TIPP-SD is close to the best of these methods. Finally, although TIPP-SD is slower than Kraken2 and Bracken, it is still fast enough to be used on large datasets.

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Shen, C., Wedell, E., Pop, M., Warnow, T.. 2025-09-01. TIPP-SD: A New Method for Species Detection in Microbiomes. https://doi.org/10.1101/2025.08.27.672749

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