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-## Introduction
+## pathogenseq
 
 <!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
 **pathogenseq** is a pathogen whole genome sequence (WGS) data analysis pipeline, which inclues sequence quality checking, quality control, taxonomy assignment, assembly, assembly quality assessment, assembled contig annotation, mlst, antimicrobial resistance, virulome, plasmid, and taxonomy prediciton.