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Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.

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Detecting Single Nucleotide Polymorphisms in Mycobacterium orygis for the Creation of Standardized Diagnostic Markers

Variant Barcoding of Mycobacterium orygis

What is Mycobacterium orygis?

Mycobacterium orygis is an overlooked member of the Mycobacterium tuberculosis complex (MTBC). M. orygis had initially been detected in animals such as oryxes, cattle, antelopes, and rhesus monkeys. However, M. orygis has recently been isolated in patients presenting with tuberculosis from South Asia (Bangladesh, India, Nepal, and Pakistan). M. orygis has no accepted markers for identifying and tracking, which is a point of concern for rapid clinical diagnosis and epidemiological tracking.

What is variant barcoding?

Variant barcoding is an in silico technique that uses nucleotide markers, such as single nucleotide polymorphisms (SNPs), to distinguish variants.

Our hypothesis:

We hypothesize that by using the variant barcoding methodology and validating our findings through Polymerase Chain Reaction and Sanger Sequencing, we would identify M. orygis specific SNPs that can be used as standard markers for M. orygis detection.

Pipeline for Variant Barcoding of Mycobacterium orygis:

Pipeline detailing the various steps involved in quality checking, data clean-up, SNP generation and visualization, and phylogenetic tree generation and visualization. This pipeline has been modified and adapted to suit this project from the BAGEP pipeline (Source: BAGEP GitHub).

Pipeline Honours