amplicon-nf: A nextflow pipeline for viral amplicon sequencing data

Description

artic-network/amplicon-nf is a bioinformatics pipeline that takes sequencing reads generated from ARTIC-style viral amplicon sequencing schemes, assembles them into consensus sequences, and runs some basic quality control on the outputs.

Full documentation for running the pipeline on the command-line is available in the github repository, however, if you prefer to utilise a GUI, we have SOPs for running the pipeline using EPI2ME available below.