PhaVa is an approach for finding potentially Phase Variable invertible regions, also referred to as invertons, in long-read seqeuncing data
The PhaVa workflow is divided into three steps: locate, create, and ratio.
phava locate -i genome.fasta -d out_dir
phava create -d out_dir
phava ratio -r long_reads.fastq -d out_dir
Alternatively, all three steps can be run in a single command via variation_wf
phava variation_wf -i genome.fasta -r long_reads.fastq -d out_dir
Output from each step is centered around a output directory (-d) and should be the same directory for the entire workflow The locate and create steps only need to be performed once for a given genome or metagenome, and ratio can then be run on long-read samples using the same output directory (-d)
git clone https://github.com/patrickwest/PhaVa