A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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use ivar default of 30 for illuminaKeepLen in Sanger config #61
This is more appropriate for libraries created by ligating adapters on the end of the amplicon (than when tagmentation is used as with many other Illumina pipelines)
Thinking aloud, but maybe the default for this should be set dynamically based on whether we're keeping reads without primers (proxy for Nextera/Ligation).
This is more appropriate for libraries created by ligating adapters on the end of the amplicon (than when tagmentation is used as with many other Illumina pipelines)