Using snpgenie

The program includes both a command line and graphical interface. Both will produce the same results.

Command Line

This will run the entire process based on a set of options given at the terminal:

-h, --help            show this help message and exit
-i FILE, --input FILE
                      input folder(s)
-l FILE, --labels FILE
                      sample labels file, optional
-r FILE, --reference FILE
                      reference genome filename
-w, --overwrite       overwrite intermediate files
-m, --trim            trim fastq files
-q QUALITY, --quality QUALITY
                      trim quality
-t THREADS, --threads THREADS
                      cpu threads to use
-o FILE, --outdir FILE
                      Results folder
-v, --version         Get version
-s, --test            Do test run

Example:

snpgenie -r reference.fa -g reference.gff -i data_files -t 8 -o results

From Python

You can run a workflow from within Python:

from sngenie import app
args = {'threads':8, 'outdir': 'results', 'labelsep':'-',
        'input':['/my/folder/',
                 '/my/other/folder'],
        'reference': None, 'overwrite':False}
W = app.WorkFlow(**args)
st = W.setup()
W.run()

Desktop Application

This interactive tool is designed for those not comfortable with the command line and includes some additional features such as visualization of fastq qualities.