Differences between Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex), Nextera DNA, and Nextera XT kits

**What are the differences between Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) and other Nextera Library prep kits?**Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) library prep kit provides the flexibility of use across a wide range of genomes from small genomes (microbial genomes, amplicons) to more complex genomes (eukaryotes and human).

Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) library prep is rooted in an innovative bead-linked transposome (BLT) complex that tagments genomic DNA by fragmenting and adding adaptor tag sequences in a single reaction step. Once saturated with input DNA, the BLT complex fragments a set number of DNA molecules, providing flexibility to use a wide DNA input range, consistently tight fragment size distribution, and normalized libraries.

**Is Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) compatible with Nextera DNA or Nextera XT indexes?**Although they share sequence compatibility, it is not recommended to use XT indexes with Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) libraries as Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) has indexes of higher purity that have been carefully optimized for improved performance.

**Is Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) compatible with Nextera DNA or Nextera XT reagents?**No, Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) reagents are not compatible with Nextera DNA or Nextera XT reagents as the enzymatic chemistry is very different from that of Nextera DNA and Nextera XT.

**As performed with Nextera XT, can we perform bead-based normalization (BBN) with Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) libraries?**Normalization in Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) happens during tagmentation, hence there is no need to perform bead-based normalization at the end of library prep. Furthermore, Nextera XT bead-based normalization process is not compatible for use with Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex).

**What happens if a customer uses Nextera XT’s BBN reagents with Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex)?**This will not produce viable sequencing libraries. The Nextera XT reagents are not compatible for use with the Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) protocol.

**Can we use Nextera libraries for downstream enrichment capture?**No. Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) chemistry is incompatible with the enrichment chemistry. The Illumina DNA Prep with Enrichment (S) Tagmentation library prep kit is recommended instead.

For any feedback or questions regarding this article (Illumina Knowledge Article #1256), contact Illumina Technical Support [e-mail].