Difference between revisions of "Platon"
| Line 61: | Line 61: | ||
<!--Citation--> | <!--Citation--> | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
| − | If you publish research that uses {{#var:app}} you have to cite it as follows: | + | If you publish research that uses {{#var:app}} you have to cite it as follows:<br> |
| + | <code>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</code> | ||
| + | <br> | ||
| + | <br> | ||
| + | As Platon takes advantage of the inc groups, MOB HMMs and oriT sequences of the following databases, please also cite:<br> | ||
| + | <code>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</code> | ||
| − | + | <code>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</code> | |
| − | + | <code>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</code> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Latest revision as of 17:14, 14 December 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