An automated analysis pipeline PHANtAsTiC: Public Health Analysis of Nucleotides through Assembly, Typing and Clustering Version 3.0
The pipeline is implemented as a Galaxy (https://galaxyproject.org/) workflow integrated with an IRIDA (https://www.irida.ca/) instance. The tool performs performs trimming (Trimmomatic) and assembly (SPAdes or INNUca), typing and clustering elaborations in basis of the type of file (single-end reads versus paired-end reads) and bacterial species (E. coli or Listeria). In our environment the pipeline is executed on a dedicated Galaxy instance through an API call, analysing directly the sequences uploaded in IRIDA. For more information see: http://biorxiv.org/lookup/doi/10.1101/2020.05.14.095901