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A flexible pipeline for complete analysis of bacterial genomes
A curated collection of Nextflow implementation patterns
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
A pipeline for bioinformatics analysis of bacterial genomes
A bioinformatics pipeline to phase and impute genetic data
The Metagenomics-Toolkit is a scalable, data agnostic workflow that automates the analysis of short and long metagenomic reads obtained from Illumina or Oxford Nanopore Technology devices, respecti…
A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge
A simple pipeline for bacterial assembly and quality control
Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.
Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.
Nextflow pipeline for pathogen surveillance in wastewater
cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.
Locally deployable search tool to explore local Salmonella epidemiology in a global context
Pipeline for submitting data to INSDC databases for IRIDA Next