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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: software resource, software toolkit, source code
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,
Availability: Free, Available for download, Freely available
Resource Name: pathogensurveillance
Resource ID: SCR_028493
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Source: SciCrunch Registry (RRID:SCR_005400)
Description: Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.
URL: https://rrid.site/rin/sources/SCR_005400
