Abstract: The disclosure provides for hybrid protocols and barcoding schemes that allow for sequencing of targeted polynucleotides in multiple types of sequencing platforms, and applications thereof, including for metagenomic analysis.

Abstract: The present disclosure provides methods for characterizing a target DNA present in a sample. The methods involve contacting the sample with a type V CRISPR/Cas effector protein and one or more guide RNAs, where the contacting generates a cleavage product comprising a 5? overhang; and ligating a double-stranded nucleic acid adapter to the cleavage product, to generate a ligation product. The ligation product includes the target DNA, which can be sequenced. The sample can be subjected to one or more amplification steps prior to the contacting step, with primers that provide for amplification of nucleic acids of, e.g., specific pathogens, categories of pathogens, two or more different pathogens, or two or more different categories of pathogens.

Abstract: Methods, compositions and kits for detection of a taxon of pathogenic microorganisms in a sample are provided. Also provided are methods, compositions and kits for detecting taxons of pathogenic microorganisms present in low titers in a sample. Compositions, methods and kits for detection of pathogenic co-infections are also provided.