Install

In this instance, AntiSMASH was run using the official docker image. Docker was installed following these instructions; AntiSMASH was installed following these instructions for antiSMASH stand alone. The docker version used was 1.13.1, build 092cba3; the AntiSMASH version used was 3.0.5.

Running AntiSMASH

AntiSMASH was run on a GenBank formatted file of all annotated chromosomes derived from GenBank:

sudo /path/to/run_antismash sequences.gb output

This will create an output directory that contains various outputs, including a 'geneclusters.txt' flat text file. A Python script was used to collect the gene IDs for clusters:

python getClusters.py -i geneclusters.txt > geneclusters_ids.txt

Then for each snp summary file from snpEff (see previous section), this script.

bash grepClusters.sh geneclusters_ids.txt output