Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics

Abstract

Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature and computational complexity. In Bioinformatics, k-mer-based approaches were long established to expedite the analysis of large sequencing data and are now widely used to annotate metagenomic data. We make use of k-mer counting techniques for efficient and accurate compositional analysis of microbiota from whole metagenome sequencing. Mibianto solves this problem by operating directly on read files, without manual preprocessing or complete data exchange. It handles diverse sequencing platforms, including short single-end, paired-end, and long read technologies. Our sketch-based workflow significantly reduces the data volume transferred from the user to the server (up to 99.59% size reduction) to subsequently perform taxonomic profiling with enhanced efficiency and privacy. Mibianto offers functionality beyond k-mer quantification; it supports advanced community composition estimation, including diversity, ordination, and differential abundance analysis. Our tool aids in the standardization of computational workflows, thus supporting reproducibility of scientific sequencing studies. It is adaptable to small- and large-scale experimental designs and offers a user-friendly interface, thus making it an invaluable tool for both clinical and research-oriented metagenomic studies. Mibianto is freely available without the need for a login at: https://www.ccb.uni-saarland.de/mibianto.