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Updated results available for kSNP3 phylogenetic tree

Clinton requested addition of reference genomes (Burkholderia cepacia, Pseudomonas fluorescens, Pseudomonas putida) to be added to phylogenetic tree
Added by Katie Lennard almost 6 years ago

The alignment.nf module was edited so that additional reference genomes could be added to the pipeline and used to generate kSNP3 phylogenetic trees with the new --user_genome_paths flag. Users can now optionally also add draft contigs (as opposed to running kSNP3 on freebayes-generated consensus seqs.


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