The sippr pipeline is designed to run with a minimum of three supplied parameters:
* path in which report folder is to be created (-o)
* path to FASTQ sequence data (-s)
* path to reference database (-r)
sippr.py -o /output/path -s /sequence/path -r /reference/target/path
usage: sippr.py [-h] -o OUTPUTPATH -s SEQUENCEPATH [-r REFERENCEFILEPATH]
[-n NUMTHREADS] [-u CUSTOMCUTOFFS] [-S]
Perform modelling of parameters for GeneSipping
optional arguments:
-h, --help show this help message and exit
-o, --outputpath OUTPUTPATH
Path to directory in which report folder is to be
created
-s, --sequencepath SEQUENCEPATH
Path of .fastq(.gz) files to process.
-r, --referencefilepath REFERENCEFILEPATH
Provide the location of the folder containing the
pipeline accessory files (reference genomes, MLST
data, etc.
-n, --numthreads NUMTHREADS
Number of threads. Default is the number of cores in
the system
-u, --customcutoffs CUSTOMCUTOFFS
Custom cutoff values
-S, --serotype Perform serotype analysis on samples determined to be
Escherichia