PathoLive-Real-Time Pathogen Identification from Metagenomic Illumina Datasets.

ABSTRACT: Over the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics. Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing has finished. The interpretation of results can further be challenged by contaminations, clinically irrelevant sequences, and the sheer amount and complexity of the data. We implemented PathoLive, a real-time diagnostics pipeline for the detection of pathogens from clinical samples hours before sequencing has finished. Based on real-time alignment with HiLive2, mappings are scored with respect to common contaminations, low-entropy areas, and sequences of widespread, non-pathogenic organisms. The results are visualized using an interactive taxonomic tree

SUBMITTER: Tausch SH 

PROVIDER: S-EPMC9505849 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature