Query Regarding xGen FFPE Kit Settings Duplex vs Dual UMI

[npatel-ah]

Hello,

I am planning to use the FastQuorum pipeline to analyze human WES samples sequenced using IDT's xGen cfDNA & FFPE DNA Library Prep Kit.

In the FastQuorum documentation, the strand setting is listed as "Dual" for this kit. However, based on the kit description, I believe it employs Dual UMIs on a single strand. According to IDT's analysis guidelines:

"The xGen cfDNA & FFPE DNA Library Prep Kit is designed specifically for 1–250 ng of degraded samples, such as cell-free DNA (cfDNA) or DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. The method features a proprietary single-stranded ligation strategy that maximizes conversion, suppresses adapter-dimer formation, and reduces chimera rates."

Could you please confirm whether the appropriate setting for this kit in FastQuorum should account for its single-strand ligation strategy?

I understand this is not listed as verified on FastQuorum documentation, but I would appreciate your insights to ensure optimal analysis.

Thank you in advance!

Best regards
Nihir

[SPPearce]

The document suggests the template is +8M143T +8M143T, which means it has an 8bp barcode at the start of each read, so classes as Dual stranded. The document doesn't mention that it can be used for duplex sequencing, but I think it is; you could try setting the duplex option on (if it isn't duplex suitable you'll know when you get almost no reads back).