This is a python program designed for Species identification and strain attribution with unassembled sequencing data.
module spider pathoscope to find out what environment modules are available for this application.
- HPC_PATHOSCOPE_DIR - installation directory
- HPC_PATHOSCOPE_BIN - executable directory
- HPC_PATHOSCOPE_REF - reference directory
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.