Difference between revisions of "Platon"

Revision as of 15:17, 19 August 2022

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.

Environment Modules

Run module spider platon to find out what environment modules are available for this application.

System Variables

HPC_PLATON_DIR - installation directory
HPC_PLATON_DIR - executable directory
PLATON_DIR - reference 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:

       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

       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

       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

@@ Line 1: / Line 1: @@
 [[Category:Software]]
-[[Category:Bioinformatics]]
+[[Category:Biology]]
 [[Category:Sequencing]]
 [[Category:Biology]]