Difference between revisions of "Pathoscope"
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Sequencing]][[Category:Genomics]][[Category:Biology]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|pathoscope}} | |{{#vardefine:app|pathoscope}} | ||
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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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: | ||
| − | + | Hong, Changjin, et al. “PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.” Microbiome 2.1 (2014): 1-15. | |
| + | |||
| + | Byrd, Allyson L., et al. “Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.” BMC bioinformatics 15.1 (2014): 262. | ||
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| + | Francis, Owen E., et al. “Pathoscope: Species identification and strain attribution with unassembled sequencing data.” Genome research 23.10 (2013): 1721-1729. | ||
|}} | |}} | ||
Latest revision as of 17:02, 21 August 2022
Description
This is a python program designed for Species identification and strain attribution with unassembled sequencing data.
Environment Modules
Run module spider pathoscope to find out what environment modules are available for this application.
System Variables
- HPC_PATHOSCOPE_DIR - installation directory
- HPC_PATHOSCOPE_BIN - executable directory
- HPC_PATHOSCOPE_REF - reference directory
Citation
If you publish research that uses pathoscope you have to cite it as follows:
Hong, Changjin, et al. “PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.” Microbiome 2.1 (2014): 1-15.
Byrd, Allyson L., et al. “Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.” BMC bioinformatics 15.1 (2014): 262.
Francis, Owen E., et al. “Pathoscope: Species identification and strain attribution with unassembled sequencing data.” Genome research 23.10 (2013): 1721-1729.