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fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
Romain Derelle1, John Lees2,3, Jody Phelan4
1NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London W2 1PG, United Kingdom.
Summary:
Fastlin is a bioinformatics tool designed for rapid Mycobacterium tuberculosis complex (MTBC) lineage typing. It utilizes an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms associated with specific MTBC lineages. In a comprehensive benchmarking against existing tools, fastlin demonstrated high accuracy and significantly faster running times.
Availability And Implementation:
fastlin is freely available at https://github.com/rderelle/fastlin and can easily be installed using Conda.
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Causative Organism
The primary infectious agent causing tuberculosis is Mycobacterium tuberculosis, a slow-growing, acid-fast, aerobic rod that exhibits sensitivity to heat and ultraviolet light. Instances of Mycobacterium bovis and Mycobacterium avium contributing to the development of TB infection are rare.
Mode of...