Viral-Read-Detection

using INVADEseq to detect viral reads from scRNA-seq data

run_cellranger.pbs

code to obtain cellranger output files for a sample starting from the .fastq sequencing files

pathseq_process.pbs:

This will process subfolders of the raw_data_folder where cellranger output should be located. Output will take the names of these subfolders. This script was adapted from Visium_pipeline.sh and uses INVADEseq.py.

These files were retrieved from the INVADEseq GitHub: https://github.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/

The pathseq reference database can be found on https://console.cloud.google.com/storage/browser/gatk-best-practices/pathseq/resources

INVADEseq.py

this code is used when running pathseq_process.pbs

scRNAseq_pipeline_SeuratV4_Narmada2024_PATHSEQ.R

Code to reproduce the seurat object. The processed seurat object can be downloaded from https://zenodo.org/records/13643041

Reference

When using this code, please cite Van Renne et al. 2024 PLoS One (in press) and the INVADEseq authors: Galeano-Niño et al., 2022 Nature.