piggy 1.5

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$ which piggy
/local/cluster/bin/piggy
$ piggy --version
1.5

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$ piggy --help

Piggy - version 1.5

--in_dir|-i     <STR>   input folder [default - current folder]
--out_dir|-o    <STR>   output folder [default - current folder/piggy_out]
--roary_dir|-r  <STR>   folder where roary output is stored [required]
--threads|-t    <INT>   threads [default - 1]
--nuc_id|-n     <INT>   min percentage nucleotide identity [default - 90]
--len_id|-l     <INT>   min percentage length identity [default - 90]
--edges|-e              keep IGRs at the edge of contigs [default - off]
--size|-s       <STR>   size of IGRs to extract [i-j] [default 30-1000]
--method|-m     <STR>   method for detecting switched IGRs [g - gene_pair, u - upstream] [default - g]
--R_plots|-R            make R plots (requires R, Rscript, ggplot2, reshape2) [default - off]
--fast|-f               fast mode (doesn't align IGRs or detect switched regions) [default - off]
--help|-h               help
--version|-v            version