> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/library-preparation/dna-library-prep/library-preparation-dna-library-prep-faq-list/000001256.md).

# Differences between the Illumina DNA Prep (M) Tagmentation and Nextera XT kits

\*\*What are the differences between Illumina DNA Prep (M) Tagmentation (Nextera DNA Flex) and Nextera XT kit?\*\*Illumina DNA Prep (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 uses a 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 compatible with Nextera XT indexes?\*\*Although they share sequence compatibility, it is not recommended to use XT indexes with Illumina DNA Prep (Nextera DNA Flex) libraries as Illumina DNA Prep (Nextera DNA Flex) has indexes of higher purity that have been carefully optimized for improved performance.

\*\*Is Illumina DNA Prep compatible with Nextera XT reagents?\*\*No, Illumina DNA Prep reagents are not compatible with Nextera XT reagents as the enzymatic chemistry is very different from that of Nextera XT.

\*\*As performed with Nextera XT, can bead-based normalization (BBN) be used with Illumina DNA Prep libraries?\*\*Normalization in Illumina DNA Prep happens during tagmentation when inputs of 100 - 500 ng are used, hence there is no need to perform bead-based normalization at the end of library prep. Further, the Nextera XT bead-based normalization process is not compatible for use with Illumina DNA Prep.

\*\*What would happen if Nextera XT BBN reagents were used with Illumina DNA Prep?\*\*This will not produce viable sequencing libraries. The Nextera XT reagents are not compatible for use with the Illumina DNA Prep protocol.

\*\*Can Illumina DNA Prep libraries be used for downstream enrichment capture?\*\*No. Illumina DNA Prep chemistry is incompatible with enrichment chemistry. The Illumina DNA Prep with Enrichment (S), Tagmentation library prep kit is recommended instead.\
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1256), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001256%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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