This project provides a Snakemake pipeline for analyzing the transcriptome of Human Cytomegalovirus (HCMV) across two conditions (2 days post-infection and 6 days post-infection).
To run this pipeline, you must have the following tools installed: Python 3.x, Snakemake, Biopython, Kallisto, Sleuth (R package), Bowtie2, SPAdes, NCBI Datasets CLI, BLAST+.
If using Conda, you can install most dependencies with:
conda install -c bioconda snakemake kallisto bowtie2 spades blast-plus biopython
To install R, use the following link: R website
- Clone this repository:
git clone https://github.com/sofiaorellanar-boop/Comp_Bio_project.git
cd Comp_Bio_project
- Place your raw fastq files in a directory named data/ (test data set is already included).
- Ensure your metadata.txt file is present in the main directory. It should look something like this with tab delimited spaces:
- Run the pipeline using Snakemake:
snakemake --cores 4