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.
amplicon-nf EPI2ME SOPs
amplicon-nf: Running the pipeline in EPI2ME
Using EPI2ME for running the ARTIC amplicon-nf pipeline without the commandline
amplicon-nf: Viewing outputs of the pipeline in EPI2ME
Viewing outputs of the amplicon-nf pipeline in EPI2ME