#SigSeekr Unique Strain-Specific Python Probe Identifying Program
##Requirements
- rMLST data from PubMLST (requires an account) in *.fasta format
- Genomes folder in your working directory containing *.fa files
- Target Genome(s)
- BLASTn and Biopython
##Purpose Allows the user to find probes that will differentiate between closely related genomes. rMLST is required for the software to run typing methods. A mass downloader is recommended for downloading rMLST genes
##Use Core.py is the main handler for typing and unique sequence searching methods
-
Output folder where a csv typing file and Unique sequences folder will be placed
(-o, --output) -
Input folder containing Genomes folder
(-i, --input) -
Markers folder containing all 53 rMLST markers in fasta format
(-m, --markers) -
Other markers may be used as well, anything to differentiate genomes or proteins
- Evalue start (default 1e-40)
(-e, --evalue) - Evalue stop (default 1e-90)
(-s, --estop)
Core.py -o USS_Ppip/ -i USS_Ppip/ -m /rMLST/ -t Ecoli_EDL933.fa