Core genome pipeline scripts
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pileup
reads
scripts
README.md
generate_core_alignment.sh
generate_phylogeny.sh
generate_pileup.sh
prepare_for_pileup.sh
remove_recombination.sh

README.md

WGS-Pipeline

Core genome pipeline scripts for the generation of a maximum likelihood phylogeny from whole genome sequencing reads. Detailed instructions for running this pipeline are located at: http://gall-id.cgrb.oregonstate.edu/wgs-id.html