nf-core

nf-core/pathogensurveillance

Surveillance of pathogens using population genomics and sequencing

61 stars 9 forks 61 watchers Nextflow MIT License

biosurveillance nextflow nf-core pathogen-identification pipeline workflow

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2 Open Issues Need Help Last updated: Jul 28, 2026

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Add header to FIND_ASSEMBLIES output 1 day ago

enhancement good first issue

nf-core/pathogensurveillance

61

Surveillance of pathogens using population genomics and sequencing

Nextflow

#biosurveillance#nextflow#nf-core#pathogen-identification#pipeline#workflow

Add alternative to `report_group_ids` column that takes column names to base groups on 9 days ago

good first issue

nf-core/pathogensurveillance

61

Surveillance of pathogens using population genomics and sequencing

Nextflow

#biosurveillance#nextflow#nf-core#pathogen-identification#pipeline#workflow