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MIRUReader: MIRU-VNTR typing directly from long sequencing reads
Cheng Yee Tang1, Rick Twee-Hee Ong1
1Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 117549 Singapore.
Summary:
Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is widely used to genotype Mycobacterium tuberculosis complex in epidemiological studies for tracking tuberculosis transmission. Recent long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore Technologies 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 MIRU-VNTR typing directly from long sequence reads.
Availability And Implementation:
Source code and documentation for MIRUReader program is freely available at https://github.com/phglab/MIRUReader.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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