MIBiG & References

Providing reference .gbks, tldr: pre antiSMASH processed MIBiG gbks (stored in the dl.secondarymetabolites.org/mibig/ repo) are given via -m, any ‘normal’ antiSMASH processed .gbks can be given via either -m or -r.

Note: antiSMASH processed files of recent MIBiG releases might not be immediately available. In that case, you must first process it with antiSMASH.

If desired, BiG-SCAPE 2 can make use of two types of (antiSMASH processed) references: MIBiG .gbk files and user defined reference .gbk files.

To make use of the MIBiG repository, toggle the --mibig option to ensure the appropriate antiSMASH-processed .gbk files are used. Doing this for the first time will download these files (from the dl.secondarymetabolites.org/mibig/ repo) in the BiG-SCAPE 2 local directory (e.g. ./BiG-SCAPE/MIBiG/mibig_antismash_3.1_gbk). Currently only MIBiG versions 3.1 and up are available with this method.

The MIBiG gene cluster .gbk files in this repo have been processed by a custom antiSMASH version so that even BGCs in the MIBiG database that do not trigger an antiSMASH rule, and would not otherwise be detectable/outputted by antiSMASH, are able to be used with BiG-SCAPE 2. The .gbk files processed with this specific antiSMASH version will have slight differences in content vs .gbk files processed with a ‘common’ version of antiSMASH, which makes the differentiation between --mibig_version and --reference_dir necessary.

Any custom set of these custom antiSMASH processed MIBiG .gbks, such as a subset of files, can also be used by placing these files in ./BiG-SCAPE/MIBiG/mibig_antismash_[any_string]_gbk and running with --mibig-version [any_string].

Any user-defined reference gene cluster .gbks that have been processed by a ‘common’ antiSMASH run can be provided with --reference-dir.

If a user wants to provide a (older) version of antiSMASH processed MIBiG that is not available from the dl.secondarymetabolites.org/mibig/ repo and thus already pre-processed with the custom antiSMASH version, and wishes to download MIBiG and process it with antiSMASH in house, these .gbk files can in theory be provided via either --mibig-version or --reference-dir.

Providing non-antiSMASH processed user defined reference .gbk files is possible by toggling the --force-gbk option. Nevertheless, BiG-SCAPE 2 still requires CDS and Sequence features to be present in these .gbk files.

Finally, reference BGC record nodes will feature a blue edge in the interactive visualization network, and connected components that contain uniquely reference BGC records, as well as reference singletons, will not be displayed in the output interactive visualization or output tsv files, or saved to the database.