We are starting to run 10X libraries on a Nova-seq and there are some issues with the current indexing primers that make them unideal for the Nova-seq platform.
First, 10x libraries are single indexed. At scale, there are simply too many samples that would be put on a Nova-seq flow cells for single-indexes to be useful as they will likely collide with other libraries.
Second, indexes on the Nova-seq should not start with GG, because the Nova-seq is a two-color machine and G is the dark cycle; sometimes indexes that start GG can fail.
I request that you move quickly to using dual 8 base indexes. There is minimal downside and it would future proof your libraries to be compatible with the Nova seq.
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