dragonSMASH

Bash pipeline for bacterial genome assembly, annotation, BGC detection, and self-resistance mining.

Runs Oxford Nanopore assemblies through 9 stages: assembly (Dragonflye), QC (SeqKit), annotation (Bakta), BGC detection (antiSMASH 8), 16S taxonomy (barrnap + Kraken2), whole-genome taxonomy (GTDBTk), BGC novelty scoring (SCALES), and self-resistance gene discovery (DRACS).

Install

• MDU server users (trillian / marvin / zaphod): docs/INSTALL_mdu.md
• External users (your own conda): docs/INSTALL_external.md
• Spartan / HPC: docs/INSTALL_spartan.md

Quick start:

git clone https://github.com/sharkeylkr/dragonSMASH.git
cd dragonSMASH
bash setup/setup.sh

Documentation

Pipeline stages, configuration options, output structure, and usage examples are in the relevant install guide above.

DRACS (self-resistance discovery) is based on ARTS (Ziemert lab). SCALES (BGC novelty scoring) is an original module.

License

GPL-3.0-or-later. See LICENSE.

DRACS includes code derived from ARTS, copyright (C) 2015, 2016 Mohammad Alanjary, licensed under GPL-3.0.

Citation

If you use dragonSMASH, please cite the underlying tools:

• Dragonflye: github.com/rpetit3/dragonflye
• Bakta: Schwengers et al. (2021) Microbial Genomics doi:10.1099/mgen.0.000685
• antiSMASH: Blin et al. (2023) Nucleic Acids Research doi:10.1093/nar/gkad344
• ARTS: Ziemert et al. (2020) Mungan,M.D., Alanjary,M., Blin,K., Weber,T., Medema,M.H. and Ziemert,N. (2020) ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Res.,10.1093/nar/gkaa374
• GTDBTk: Chaumeil et al. (2022) Bioinformatics doi:10.1093/bioinformatics/btac672
• Kraken2: Wood et al. (2019) Genome Biology doi:10.1186/s13059-019-1891-0