scVirusScan: A method for swift and accurate detection of viral pathogens in single-cell RNA datasets
sc-VirusScan is a method that enables accurate, sensitive and scalable detection of viral pathogens in single-cell RNA datasets.
The sc-VirusScan integrates the strengths of two standard approaches, a standard mapping based approach and a Kraken2 k-mer based approach which provides rapid taxonomic classification. The output of the sc-VirusScan pipeline can be integrated easily into existing single cell analysis frameworks (Seurat and Scanpy) which can provide standardized and reliable way to scrutinize virus infections at the single cell level resolution.
sc-VirusScan by installed by following the below mentioned steps.
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Clone the Git Repository using: git clone https://github.com/maxplanck-ie/sc-VirusScan.git
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Change the directory to sc-virus-scan:
cd sc-VirusScan -
The dependecies of sc-VirusScan can be installed from the provided env.yaml by using conda/mamba
mamba env create -f env.yaml -n sc-VirusScan -
Additionally, this pipeline needs
CellRangertool. To install CellRanger please refer to https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation -
Upon successfull installation of CellRanger, the CellRanger path needs to be updated in the
config.yamlfile accordingly -
Lastly, the
config.yamlneeds to be modified as per your system environment variables. More information aboutconfig.yamlalong with its description can be found in the Read the docs page.
For detailed documentation on setup and usage, please visit our Read the docs page.
sc-VirusScan was developed by Saim Momin as a Master Thesis project for the Bioinformatics Master program of the Saarland University, under the supervision of Deboutte W and Manke T. at the Bioinformatics Unit of the Max Planck Institute for Immunobiology and Epigenetics in Freiburg.
sc-VirusScan pipeline is under active development. Please use issues to the GitHub repository for feature requests or bug reports.