MycoSNP

MycoSNP performs whole-genome sequencing (WGS) analysis of fungal organisms, focusing on reference selection, read alignment, SNP calling and filtration to support genomic surveillance of Candida auris.

Key Features:

• Portable Workflow: Workflow packaged for deployment across computational platforms.
• Reference Selection and Preparation: Incorporates methods for selecting and preparing reference genomes to support accurate alignment.
• Quality Assessment and Control: Applies stringent quality assessment and control to sequencing reads.
• Read Alignment: Aligns sequencing reads to reference genomes using advanced alignment algorithms.
• SNP Calling and Filtration: Calls single-nucleotide polymorphisms and applies filtration to identify genetic variation relevant to pathogen evolution and drug resistance.

Scientific Applications:

• Molecular Surveillance of Candida auris: Enables genomic surveillance to track global spread and investigate local outbreaks of Candida auris.
• Epidemiology and Transmission Dynamics: Supports monitoring of epidemiological trends and inference of transmission dynamics using comparative SNP analysis.
• Antimicrobial Resistance Research: Facilitates identification of genetic variants associated with drug resistance mechanisms in Candida auris.

Methodology:

Reference genome selection and preparation, sequencing read quality assessment and control, read alignment to reference genomes, and SNP calling and filtration.