Replication Data and Scripts : ViroSeek a viral detection pipeline for second-generation sequencing

This repository contains all the files needed to reproduce the results of the article "ViroSeek: a viral detection pipeline for second-generation sequencing", including the files needed to run the ViroSeek pipeline. ViroSeek is a simplified bioinformatics pipeline for the taxonomic analysis of second-generation sequencing data. It contains: Main pipeline scripts (bash or nextflow) for automated execution of the steps Installation instructions and README file describing the software prerequisites (FastQC, TrimGalore, BBTools, SPAdes, Samtools, TaxonKit), as well as the yml file for setting up the conda environment. Bash script for generating simulated data with CASIMIM, used as a positive sample in the article. R script used for downstream pipeline analysis