ViralCellDetector

This R script can be used to detect virus infection in cell lines. It takes the input as raw RNA-seq reads as input and provide the list of putative viruses as output. The final virus could be visualized by the igv genome viewer.

Installation

git clone https://github.com/Bin-Chen-Lab/ViralCellDetector

## Then go to the ViralCellDetector directory:
cd ViralCellDetector

Usage

First user need to run the Genome_index.sh bash code

bash Genome_index.sh
## This will download the Human genome and Viral genomes required for the script.

To use the script, you will need to have R and the necessary packages installed. Once you have the dependencies set up, you can run the script by calling following code

## basic example code
Rscript ViralCellDetector sample_input.txt
## The sample_inpit.txt file is the file containing the name of fastq input files. If a fastq input file is "input_file_1.fq and input_file_2.fq", then "sample_input.txt" file should have "input_file" name in first row.

Input

The script takes as input as RNA-seq raw sequencing fastq file, Users need to create a fastq directory in the ViralCellDector directory and put all their fastq files in the fastq directory. Then user need to creat a sample_input.txt file and enter all fastq files name in it. If fastq files are paired end then their only name should be provided in sample_input.txt as mentioned in example code. The ViralCellDetector prefer to accept the RNA-seq data generated by the robominus approach, however user can also use the RNA-seq raw reads generated by poly-A enrichment approach.

Output

The script will output a list of names of putative viruses, which are supposed to be present in the samples.

Note

Please make sure that the sequencing reads are with good quality.

Dependencies

The script requires the following R packages and tools to be installed: samtools (https://github.com/samtools/samtools/)

STAR (https://github.com/alexdobin/STAR)

BWA (https://bio-bwa.sourceforge.net/)

dplyr (https://dplyr.tidyverse.org/)

plyr (https://cran.r-project.org/web/packages/plyr/index.html)

foreach (https://cran.r-project.org/web/packages/foreach/vignettes/foreach.html)

Parellel (https://www.rdocumentation.org/packages/parallel/versions/3.6.2)

FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

IGV (https://software.broadinstitute.org/software/igv/)

Make sure these packages are installed before running the script.

Example

To run the example files, we have provided a example code:

Run_test_ViralCellDetector.sh

Contributors

ViralCellDetector is developed by BinChen lab. Any questions or feedback can be addressed to Rama Shankar, PhD, ramashan@msu.edu or Bin Chen, PhD, PI, Chenbi12@msu.edu