FAQ: How do I analyze data from libraries generated using the NEBNext ARTIC kits for Illumina?

The sequence data produced is compatible with a number of analysis tools including https://nf-co.re/viralrecon and https://covid19.galaxyproject.org/artic/. To maximize variant calling effectiveness in this overlapping amplicon approach, it is recommended to mask primer regions on read pairs (not the reference). It is important to consider both mates when deciding which bases to consider in variant assessment. Regions of low coverage may be due to the presence of variant bases in a priming region. Adjacent amplicons can be used to differentiate between such variant-mediated events from stochastic coverage variation.