TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization.

ABSTRACT:

Introduction

The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laboratories remain a significant diagnostic challenge in medicine and public health. Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens.

Methods

TheiaEuk was designed using containerized components and written in the workflow descrip

SUBMITTER: Ambrosio FJ 

PROVIDER: S-EPMC10428623 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature