The geneSeekr has very few requirements:
- Python
- BioPython
- Sequence (genome) files
- Target files
- ?
There are three flags that must be provided when running the program from a system other than my own. These flag override hard-coded paths.
- -p - the location you want the report folder created and populated
- -s - the location of your query sequence files (must have a .fa* extension)
- -t - the location of your target sequence files (must have a .fa* extension)
There is one additional flag, which allows you to customise the analysis
- -c - the percent identity cutoff value to determine presence/absence of gene targets