cBot FAQs

No. Original manifolds do not align correctly on the new instrument.

The first time you process template DNA, try a concentration titration range to optimize the number of clusters formed. If the concentration is too low, fewer clusters are generated and result in a low sequencing yield. If the concentration is too high, clusters are too dense and can complicate data analysis. For more information, see the Sequencing Library qPCR Quantification Guide (requires a MyIllumina login) or the HiSeq Systems Denature and Dilute Libraries Guide.

For unbalanced libraries, Illumina recommends a high-concentration spike-in of PhiX control lane to create more diverse.

Unbalanced libraries contain genomes with AT or GC content of less than 40% or greater than 60%. PhiX Control v3 (catalog # FC-110-3001) is a diverse library with a mean insert size of ~375 bp, corresponding to a 500 bp library size if visualized on a Bioanalyzer.

For more information, see Using a PhiX Control for HiSeq Sequencing Runs.

For most libraries, Illumina recommends using a low-concentration spike-in (1%) of PhiX Control v3 as an in-lane positive control for alignment calculations and quantification efficiency.

Not at this time. If you are sequencing Nextera libraries, you need sequencing primers provided in the TruSeq Dual Index Sequencing Primer Box for any run types. If you are sequencing dual-indexed TruSeq HT libraries on a single-read flow cell, you need sequencing primers provided in the TruSeq Dual Index Sequencing Primer Box, Single Read.

No. The Illumina PhiX Control v3 is a separate product. The catalog number is: FC-110-3001.

Yes. The HiSeq flow cell requires the use of a cBot for clustering on the flow cell prior to sequencing.

No. Cluster generation is performed on the MiSeq System as part of the run. No other instruments are required for sequencing on the MiSeq.