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

Bioinformatics. 2023 Nov 1;39(11):btad648. doi: 10.1093/bioinformatics/btad648.


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 and can easily be installed using Conda.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Mycobacterium tuberculosis* / genetics
  • Polymorphism, Single Nucleotide
  • Software