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Welcome to the QuAISAR-H wiki!

nf-core/quaisar-H is a bioinformatics analysis pipeline that is built with nf-core best-practices. QuAISAR-H: a comprehensive pipeline for Quality control, Assembly, taxonomic Identification, Sequence typing, Annotation, and Resistance mechanisms for pathogens causing Healthcare-associated bacterial infections. This method prepares performs quality control, confirms taxa ID, sequence typing, assembles a scaffolds/contigs, and calls AMR genes, plasmids and hypervirulence genes. QuAISAR-H generates several files that are compatible with downstream analytic tools, such as those for used for phylogenetic tree-building.

QuAISAR-H was been developed to support bioinformatics capacity in public health laboratories. This pipeline will be available to run on Terra (coming Fall 2022), Nextflow tower, CLI and is incorporated into the StaPH-B toolkit (coming Fall 2022). Broad distribution of this tool will enhance both local public health capacity and national efficiency in utilizing WGS data for HAI surveillance and investigation.

This pipeline was developed in the Division of Healthcare Quality Promotion at the CDC. For if you require assistance please contact CEMB at HAISeq@cdc.gov.

Credits:

• Rich Stanton @astanton
• Nick Vlachos @nvlachos
• Alyssa Kent @alyssagkent
• Maria Diaz @MzDiaz824
• Jill Hagey @jvhagey