Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Recommendations for pixel distance when sequences are from Novaseq
We recently resequenced samples using Novaseq technology of Illumina. we are aware of the increase in optical duplicates due to the use of patterned flowcells. In the MarkDuplicates documentation 2500 is suggested for the OPTICAL_DUPLICATE_PIXEL_DISTANCE for the patterned flowcell of the Hiseq, compared to default of 100 (Nextseq).
Do you currently have any best practices recommendations to handle this? Should the value be increased and if so by how much, because of the fact that the wells in Novaseq are even more closely packed?
Thanks so a lot for any thoughts on this!