Local binary patterns as a feature descriptor in alignment-free visualisation of metagenomic data

Abstract

Shotgun sequencing has facilitated the analysis of complex microbial communities. However, clustering and visualising these communities without prior taxonomic information is a major challenge. Feature descriptor methods can be utilised to extract these taxonomic relations from the data. Here, we present a novel approach consisting of local binary patterns (LBP) coupled with randomised singular value decomposition (RSVD) and Barnes-Hut t-stochastic neighbor embedding (BH-tSNE) to highlight the underlying taxonomic structure of the metagenomic data. The effectiveness of our approach is demonstrated using several simulated and a real metagenomic datasets.