MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris.
Methods Mol Biol
; 2517: 215-228, 2022.
Article
in En
| MEDLINE
| ID: mdl-35674957
ABSTRACT
Candida auris is an urgent public health threat characterized by high drug-resistant rates and rapid spread in healthcare settings worldwide. As part of the C. auris response, molecular surveillance has helped public health officials track the global spread and investigate local outbreaks. Here, we describe whole-genome sequencing analysis methods used for routine C. auris molecular surveillance in the United States; methods include reference selection, reference preparation, quality assessment and control of sequencing reads, read alignment, and single-nucleotide polymorphism calling and filtration. We also describe the newly developed pipeline MycoSNP, a portable workflow for performing whole-genome sequencing analysis of fungal organisms including C. auris.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Candidiasis
/
Candida auris
Limits:
Humans
Country/Region as subject:
America do norte
Language:
En
Journal:
Methods Mol Biol
Journal subject:
BIOLOGIA MOLECULAR
Year:
2022
Document type:
Article
Affiliation country:
Estados Unidos