Since its introduction in the last decade, massive parallel sequencing, or “next-generation sequencing”, has revolutionized our access to genomic information, providing accurate data with increasingly higher yields and lower costs with respect to first-generation technology. Massive parallel sequencing of cDNA, or RNA-seq, is progressively replacing array-based technology as the method of choice for transcriptomics. This review describes some of the most recent applications of next-generation sequencing technology to the study of pathogenic fungi, including Candida , Aspergillus and Cryptococcus species. Several integrated approaches illustrate the power and accuracy of RNA-seq for studying the biology of human fungal pathogens. In addition, the lack of consistency in data analysis is discussed.
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