# Sequencing information for Illumina DNA Prep (M) Tagmentation libraries

**Which Illumina sequencing instruments are compatible with this library prep?** These libraries can be run on all currently available Illumina sequencing systems.\
**Should index reads be color balanced?** Yes. Refer to the [index adapters pooling guide](https://support.illumina.com/downloads/index-adapters-pooling-guide-1000000041074.html) to for appropriate index choice for the relevant sequencing platform.

**Can libraries prepared in separate batches be pooled in the same run?**\* Yes, but all libraries must to be quantified prior to pooling.

* If input DNA was at least 100 ng, libraries from each independent experiment may be pooled and quantified together prior to pooling with the second batch.
* It is not recommended to pool all samples from independent experiments or batches without quantification.

**Are data sets available?** Yes, see [BaseSpace Demo Data](https://basespace.illumina.com/datacentral) for public sequencing and analysis data (link requires BaseSpace login).\
**Which flow cell types can be used with these libraries?** This library type is compatible with all Illumina flow cell types.\
**Can Nextera XT index primers be used with Illumina DNA Prep library preparation?**\
This is not recommended or supported. Illumina recommends using either the IDT for Illumina DNA/RNA Unique Dual (UD) indexes or the Nextera DNA CD index kits. Compatible index kits are listed below the Index Adapters heading on the [product page](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-dna-flex.html).\
**Why are the sequencing intensity profiles wobbly/spiky in the first \~15 cycles of the insert reads?** This is a normal characteristic of tagmented libraries.

**What is the recommended read length for this library type?**\
2x150 bp. Some instruments require shorter reads (2x149 bp) to account for the 10 bp dual indexes when IDT for Illumina DNA/RNA UD indexes are used.\
**Can reads >2x151 bp be used on sequencers that have sequencing kits with >300 cycles (eg, the MiSeq, NovaSeq 6000, and NextSeq 1000/2000)?**\
Longer reads lengths are not supported. Longer read lengths result in lower data quality with this library type due to the fragment size distribution of the libraries.\
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