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:
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$ which piggy
/local/cluster/bin/piggy
$ piggy --version
1.5
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help message:
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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
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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