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Nextflow pipeline identifies novel pathogens in foodborne outbreak specimens, suggesting enhanced disease tracking.
Motivation nf-UnO is a pipeline implemented in Nextflow to identify novel pathogens from metagenomic shotgun sequencing of epidemiologically-related foodborne outbreak specimens. nf-UnO employs MIDAS2, metagenomic co-assembly, multiple binning programs, and read mapping to metagenomically-assembled genomes (MAGs) to detect potential etiological agents found in common across outbreak specimens. Availability https://github.com/uel3/nf-UnO.
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Guzman-Cole et al. (2025) studied this question.
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