Are indexing kits from other companies compatible with ThruPLEX and PicoPLEX library prep kits?

If full-length barcoded adapters from other companies are added by PCR, they will work with our kits (and our indexes will work with their kits). However, due to primer concentration differences, PCR cycling conditions will need to be optimized.Unique Dual Indexing [...]

Are Takara Bio indexing kits compatible with library prep kits from other companies?

If the library preparation involves ligation of full-length barcoded adapters (e.g., full-length Y-shaped adapters with a T-overhang), our indexing primers may not be efficient for PCR due to an extra base. An example of this would be the TruSeq HT (now called TruSeq CD) adapters that are added by ligation. Unique Dual Indexing [...]

What guidelines should I follow when pooling indexes?

For HiSeq®/MiSeq® instruments, Illumina uses a red laser/LED to sequence bases A and C, and a green laser/LED to sequence bases G and T. For each cycle, both the red and green channel need to be read to ensure proper image registration (e.g., A or C and G or T must be in each cycle). If this color balance is not maintained, sequencing the index read could fail. For NovaSeqTM, NextSeq®, and [...]

What should I consider when multiplexing samples?

Any samples can be multiplexed. However, to get the best results, you should consider the following: *Fragment lengths from each sample must match. Libraries of different lengths will hybridize to the flow cell at different efficiencies, which can lead to uneven sample coverage. *All samples must use the same barcoding strategy (e.g., do not mix and match single-indexed samples with [...]

Can I perform single-read runs and still obtain both index sequences?

Yes, both index sequences can be obtained from single-read runs. Please select the appropriate workflow based on the type of flow cell (e.g., single-read or paired-end) so that the correct chemistry is used. If you are using a single-read flow cell, the TruSeq® Dual Index Sequencing Primer Box, Single-Read (Illumina, Cat. # FC-121-1003) is necessary to sequence both index reads.Unique Dual [...]