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URL: https://nf-co.re/pathogensurveillance
Proper Citation: pathogensurveillance (RRID:SCR_028493)
Description: Software automated pipeline for population genomic analyses, pathogen identification, variant detection, and biosurveillance. The pipeline accepts paths to raw reads for one or more organisms and creates reports in the form of an interactive HTML document. Significant features include the ability to analyze unidentified eukaryotic and prokaryotic samples, creation of reports for multiple user-defined groupings of samples, automated discovery and downloading of reference assemblies from NCBI RefSeq, and initial identification based on k-mer sketches followed by multi gene phylogeny and SNP-based phylogeny.
Synonyms: PathogenSurveillance
Resource Type: source code, software resource, software toolkit
Defining Citation: DOI:10.1101/2025.10.31.685798
Keywords: population genomic analyses, pathogen identification, variant detection, biosurveillance, analyze unidentified eukaryotic and prokaryotic samples, creation of reports for multiple user-defined groupings of samples, automated discovery and downloading of reference assemblies from NCBI RefSeq,
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