Initially forked from here. Thank you to the awesome binder team!
Part of the Bioinformatics Virtual Coordination Network :)
Put bioinf_tools into PATH
export PATH="${PATH}:/home/jovyan/MagicCave:/home/jovyan/bioinf_tools"
Download antismash databases
download-antismash-databases
Print the antismash help menu
antismash -h
Run the simplest version of the command
antismash Sodalis_praecaptivus-fixed.gbk
Run the simplest version of the command with an assembly
antismash --genefinding-tool prodigal Sodalis_praecaptivus-fixed.fasta
Convert GenBank output file to FASTA format
bit-genbank-to-fasta -i NZ_CP006569.1.region001.gbk -o NZ_CP006569.1.region001.fasta
bit-genbank-to-AA-seqs -i NZ_CP006569.1.region001.gbk -f NZ_CP006569.1.region001.faa
Print full help menu
antismash --help-showall
Run antismash with additional analyses
antismash --genefinding-tool prodigal --fullhmmer --pfam2go --asf --cb-knownclusters --clusterhmmer --cf-create-clusters Sodalis_praecaptivus-fixed.fasta