Platon¶
Description¶
Platon detects plasmid-borne contigs within bacterial draft (meta) genomes assemblies. Therefore, Platon analyzes the distribution bias of protein-coding gene families among chromosomes and plasmids. This analysis is complemented by comprehensive contig characterizations followed by heuristic filters.
- PLATON_DB - reference database
Environment Modules¶
Run module spider platon to find out what environment modules are available for this application.
Environment Variables¶
- HPC_PLATON_DIR - installation directory
- HPC_PLATON_BIN - executable directory
Citation¶
If you publish research that uses platon you have to cite it as follows:
- Schwengers O., Barth P., Falgenhauer L., Hain T., Chakraborty T., & Goesmann A. (2020). Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microbial Genomics, 95, 295. https://doi.org/10.1099/mgen.0.000398
As Platon takes advantage of the inc groups, MOB HMMs and oriT sequences of the following databases, please also cite:
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Carattoli A., Zankari E., Garcia-Fernandez A., Voldby Larsen M., Lund O., Villa L., Aarestrup F.M., Hasman H. (2014) PlasmidFinder and pMLST: in silico detection and typing of plasmids. Antimicrobial Agents and Chemotherapy, https://doi.org/10.1128/AAC.02412-14
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Garcillán-Barcia M. P., Redondo-Salvo S., Vielva L., de la Cruz F. (2020) MOBscan: Automated Annotation of MOB Relaxases. Methods in Molecular Biology, https://doi.org/10.1007/978-1-4939-9877-7_21
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Robertson J., Nash J. H. E. (2018) MOB-suite: Software Tools for Clustering, Reconstruction and Typing of Plasmids From Draft Assemblies. Microbial Genomics, https://doi.org/10.1099/mgen.0.000206
Categories¶
biology, sequencing