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README.md

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 # PathogenTrack
 PathogenTrack is an unsupervised computational software that uses `unmapped single-cell RNAseq reads` to characterize `intracellular pathogens` at the single-cell level. It is a python-based script that can be used to identify and quantify intracellular pathogenic `viruses` and `bacteria` reads at the single-cell level.
 PathogenTrack has been tested on various scRNA-seq datasets derived from simulated and real datasets and performed robustly. The detailes are described in our paper *`Decoding Intracellular Pathogens of scRNA-seq experiments with PathogenTrack and SCKIT`*.