MIRUReader - Fast in-silico MIRU-VNTR typing directly from long sequencing reads

Motivation
Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is widely used to genotype Mycobacterium tuberculosis complex (MTBC) in epidemiological studies for tracking tuberculosis transmission. Recent long-read sequencing technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) can produce reads that are long enough to cover the entire repeat regions in each MIRU-VNTR locus which was previously not possible using the short reads from Illumina high-throughput sequencing technologies. We thus developed MIRUReader for fast in silico MIRU-VNTR typing directly from long sequence reads.

Availability
Source code and documentation for MIRUReader program is freely available at https://github.com/phglab/MIRUReader.