ArticleEnvironmental microbiome2023
POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling.
Article in Environmental microbiome, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.BMC microbiology · 2026Article
- How low can you go? Establishing detection limits for rare eukaryotes in Southern Ocean sedimentary ancient DNA.Bioinformatics advances · 2026Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients.Microorganisms · 2024Article
- Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.Microorganisms · 2023Article
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Authors and funding
3 authors.
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Abstract
We present here POSMM (pronounced 'Possum'), Python-Optimized Standard Markov Model classifier, which is a new incarnation of the Markov model approach to metagenomic sequence analysis. Built on the top of a rapid Markov model based classification algorithm SMM, POSMM reintroduces high sensitivity associated with alignment-free taxonomic classifiers to probe whole genome or metagenome datasets of increasingly prohibitive sizes. Logistic regression models generated and optimized using the Python sklearn library, transform Markov model probabilities to scores suitable for thresholding. Featuring a dynamic database-free approach, models are generated directly from genome fasta files per run, making POSMM a valuable accompaniment to many other programs. By combining POSMM with ultrafast classifiers such as Kraken2, their complementary strengths can be leveraged to produce higher overall accuracy in metagenomic sequence classification than by either as a standalone classifier. POSMM is a user-friendly and highly adaptable tool designed for broad use by the metagenome scientific community.
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