GentySpuds

A web-deployed pipeline to seek genotyping for Enterovirus.

An enterovirus is a small and enveloped mRNA virus that can cause infections in people of all ages.

Introduction

Genotyping is a way of putting a virus into categories based on similar genes. Determining the genotype of viruses is important not only in epidemiology studies, but also for efficient vaccine development and treatment

Workflow

Software Tools implemented

Installation

Usage

GentySpuds takes as input raw sequencing reads in FASTQ format, and can process gzipped files directly. nextflow run ev_gen_wf.nf -params-file params.yaml -resume
Make sure your all your fastq files are stored in one directory.