fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing

Abstract

Lineage typing of the Mycobacterium tuberculosis complex (MTBC) has evolved from traditional phenotypic methods to advanced molecular and genomic techniques. In this study we present fastlin, a bioinformatics tool designed for rapid MTBC lineage typing. Fastlin utilises an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms (SNPs) associated with specific MTBC lineages directly from fastq files. In a comprehensive benchmarking against existing tools, fastlin demonstrated high accuracy and significantly faster running times. Analysis of large MTBC datasets revealed fastlins capability not only to predict MTBC lineages, but also to detect mixed-lineage strain mixtures and estimate their proportions. Fastlin offers a user-friendly and efficient solution for MTBC lineage typing, complementing existing tools and facilitating large-scale analysis.