The NovaSeq 6000 is the latest advancement in Illumina's line of NGS sequencing instrumentation which combines high throughput patterned flow cell technology with 3 flow cell configurations while drastically reducing run times, simplifying workflow and reducing hands-on time. The NovaSeq allows the Genome Sequencing Facility (GSF) to provide increased throughput and flexibility by operating with multiple flow cell configurations. The Paired End sequencing on the NovaSeq 6000 will be available using the following flow cell configurations: S1 (0.5 Tb), S2 (1.0 Tb), S4 (3.0 Tb) - yielding 0.5 Tb - 6 Tb of sequence data per run on the dual flow cell capable sequencer. The following is a comparison of expected output and data quality for the NovaSeq 6000 flow cell options.
|Flow Cell Type||S1||S2*||S4|
|Reads Passing Filter – Single FC||1.6 B||2.8 – 3.3 B||10 B|
|2 x 100 bp||333 Gb||560–667 Gb||Not Supported|
|2 x 150 bp||500 Gb||850 – 1000 Gb||3000 Gb|
|2 x 100 bp||N/A||≥ 80%||Not Supported|
|2 x 150 bp||N/A||≥ 75%||N/A|
|2 x 100 bp||N/A||~ 25 hr.||Not Supported|
|2 x 150 bp||N/A||~ 36 hr.||~ 44 hr.|
*The NovaSeq reagent kit supporting the S1 has not been released, therefore performance metrics are subject to change. Anticipated release of S1 is Q1 2018.
Index hopping (index switching / index drift) has impacted NGS technology since the introduction of sample multiplexing. It can lead to sample misassignment of libraries from the expected index to a different index in a multiplexed pool. Slightly elevated hopping can be experienced on instruments using patterned flow cells like the NovaSeq 6000 which employ exclusion amplification chemistry (EXamp). Index hopping on a patterned flow cell system can range from 0.1 - 2% depending on the type, quality and preparation of the library. Libraries containing higher levels of unincorporated adaptors increase the risk of higher levels of index hopping. The following Best Practices will be implemented by the Genomics Core to minimize index hopping. Investigators preparing their own libraries must follow the Best Practices.
The Illumina HiSeq 2500 sequencing services provided by the Genome Sequencing Facility (GSF) allows for both the standard High Output 8 lane flow cell run and the 2 lane flow cell Rapid Run. Both services are supported by Paired-End (PE) or Single Read (SR) sequencing using the Illumina TruSeq SBS - HS and TruSeq Rapid SBS - HS chemistry. The High Output runs are available indexed or non-indexed as 50 or 100 cycle PE or SR. The Rapid Run is available indexed or non-indexed as 50, 100 or 150 cycle PE or SR. Flow cell clustering is performed using the cBOT cluster generation station. The following information is a comparison of expected output and data quality for both High Output and Rapid Read runs.
|Rapid (2 lane)||High Output (8 lane)|
|Cluster Density||750-900 k/mm2||750-850 k/mm2|
|Flow Cell Output (2x50bp)||25 - 30Gb||150Gb|
|Flow Cell Output (2x100bp)||50-60Gb||300Gb|
|Flow Cell Output (2x150bp)||75-90Gb||Not Supported|
|Bases >Q30 (2x50bp)||85%||85%|
|Bases >Q30 (2x100bp)||80%||80%|
|Bases >Q30 (2x150bp)||75%||Not Supported|
Run times between the Rapid Read and High Output are significantly different. The following provides a comparison of run times.
|Run Format||Rapid Read||High Output|
|50||~ 8 hours||~ 2 days|
|2 x 50||~ 16 hours||~ 5 days|
|2 x 100||~ 27 hours||~ 10 days|
|2 x 150||~ 40 hours||Not Supported|
Sequencing library construction is available through the GSF using the Illumina TruSeq Sample preparation kits. The following library services are offered:
For other library constructs please inquire.