# piggy 1.5


## piggy

Piggy is a tool for analysing the intergenic component of bacterial genomes. It
is designed to be used in conjunction with Roary
(https://github.com/sanger-pathogens/Roary).

Location and version:

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

help message:

```console
$ 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
```

I suggest running roary in the same directory as the input gff files, then
running piggy through with the `--roary_dir .` specified.

software ref: <https://github.com/harry-thorpe/piggy>  
research ref: <https://doi.org/10.1093/gigascience/giy015>