pathoscope¶
Description¶
Pathoscope: 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.
Environment 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, C., Manimaran, S., Shen, Y., Perez-Rogers, J. F., Byrd, A. L., Castro-Nallar, E., Crandall, K. A., & Johnson, W. E. (2014). PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome, 2(1), 33. https://doi.org/10.1186/2049-2618-2-33
- Byrd, A. L., Perez-Rogers, J. F., Manimaran, S., Castro-Nallar, E., Toma, I., McCaffrey, T., Siegel, M., Benson, G., Crandall, K. A., & Johnson, W. E. (2014). Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. BMC Bioinformatics, 15, 262. https://doi.org/10.1186/1471-2105-15-262
- Francis, O. E., Bendall, M., Manimaran, S., Hong, C., Clement, N. L., Castro-Nallar, E., Snell, Q., Schaalje, G. B., Clement, M. J., Crandall, K. A., & Johnson, W. E. (2013). PathoScope: Species identification and strain attribution with unassembled sequencing data. Genome Research, 23(10), 1721-1729. https://doi.org/10.1101/gr.150151.112
Categories¶
sequencing, genomics, biology