Scritps used for the prediction and analysis of Resistance Gene Aanalogs (RGAs)

Command lines used to run each of the softwares from the pipeline:

1) Phobius

$ perl phobius.pl -short file.fas > file.fas.phobius

2) TMHMM2

$ perl tmhmm file.fasta > file.fas.tmhmm

Note: Line 33 from the file "tmhmm" was commented, and full path was added to model on line 56.

3) Coils2

$ export COILSDIR=/path/to/coils

$ ./ncoils-osf -min_seg 1 -f < file.fas > file.fas.coils

4) PfamScan

perl pfam_scan.pl -fasta file.fas -dir ./PfamDATA/ -outfile file.fas.pfamscan

5) InterproScan

./interproscan.sh -i file.fas -f tsv

6) TargetP2

./targetp -fasta file.fas -gff3 -format short -org pl