TIPP2: metagenomic taxonomic profiling using phylogenetic markers.
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ABSTRACT: Motivation
Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample.Results
We present TIPP2, a marker gene-based abundance profiling method, that combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2, and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset.Availability and implementation
The code for our method is freely available in open source form at https://github.com/smirarab/sepp/blob/tipp2/README.TIPP.mdThe code and procedure to create new reference packages for TIPP2 are available at https://github.com/shahnidhi/TIPP_reference_package.Supplementary information
Not available online.
SUBMITTER: Shah N
PROVIDER: S-EPMC8317105 | biostudies-literature |
REPOSITORIES: biostudies-literature
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