ggHMM is a shell wrapper script that scans protein sequences downloaded from ggKbase with a provided set of HMMs. Output is a table that is ready for upload into ggKbase or further analysis by the user.
ggKbase is avalible at ggKbase
Usage and HMM import instructions are avalible at ggKbase Help
ggHMM.sh -i <input_fasta> -o <output> -m <HMM_Dir> [options]
Given a ggKbase project protein download file and a scaffold2bin file this script
will run HMMs, filter best hits, and parse the output for ggKbase upload.
Options:
-i: ggKbase project protein file (required)
-o: Directory where output files will be written (required, will be created if absent)
-m: Directory of HMM models (required)
-t: Number of threads to use (Default: 6)
-h: Display this message and exit
$./ggHMM.sh -i Example/HMM_Test.proteins.faa -o Example/Output -m Example/Test_HMMs/