Tau-typing: a Nextflow pipeline for finding the best phylogenetic markers in the genome for molecular typing of microbial species

Abstract

Abstract Summary Tau-typing is an integrated analysis pipeline for identifying genes or genomic segments whose phylogenetic resolving power most closely resembles the genome-wide resolving power of an input collection of genomes using the Kendall Tau rank correlation statistic. The pipeline is implemented in Nextflow and uses Docker and Singularity containers to ensure reliable scalability and reproducibility of results. This pipeline is particularly suitable for organisms for which whole-genome sequencing remains unaffordable or unscalable for routine applications, such as protozoan parasites which are not amenable to laboratory culture-based methods. Availability and implementation Tau-typing is freely available at https://github.com/hseabolt/tautyping. The pipeline is implemented in Nextflow with Singularity support.