This repository contains all the analysis scripts used for the publication below, which compared three different metagenomics approaches (16S, direct sequencing & sequencing after culture) with ONT's long read sequencing method to detect pathogenic Leptospira species from the environemnts:
Gorman, M., Xu, R., Prakoso, D., Salvador, L. C. M., & Rajeev, S. (2022). Leptospira enrichment culture followed by ONT metagenomic sequencing allows better detection of Leptospira presence and diversity in water and soil samples. PLOS Neglected Tropical Diseases, 16(10), e0010589. https://doi.org/10.1371/journal.pntd.0010589