NextSeq 550 FAQs

Yes. The NextSeq reagent cartridge features reservoirs specifically for Read 1, Read 2, and index custom primers. See the NextSeq System Custom Primers Guide (document # 15057456).

The loading volume is 1.3 ml and the loading concentration is 1.8 pM.

NCS v1.2 or earlier requires a different loading volume and concentration.

For more information, see the NextSeq System Denature and Dilute Libraries Guide.

The number of libraries that can be run on a NextSeq are only limited by the number of indexes available. Multiplexing of libraries allows you to pool multiple samples together while the indexes enable you to pull the data back apart (de-multiplex). Multiplexed libraries are transferred onto the flow cell from a single reservoir on the NextSeq reagent cartridge.

Sequencing an insert size of 550 bp is supported with NextSeq v2 reagents. With NextSeq v1 reagents, an insert size of 350 bp is supported.

NextSeq 500/550 kits include reagents for paired-end sequencing and a paired-end flow cell. However, single-read runs are possible on a paired-end flow cell when the run is set up as a single-read run.

The NextSeq flow cell contains four physical lanes. However, libraries are loaded onto the flow cell from a single reservoir. You can sequence a single library or multiple pooled libraries on the flow cell.

This chemistry allows us to ship the flow cells at ambient temperature. When received, store the flow cells at 2°C to 8°C.

The files are preloaded in the NextSeq Control Software (NCS). Access the files on the BeadChip Scan Configuration screen. See the NextSeq 550 System Guide (document # 15069765) . 

Supported BeadChips include the CytoSNP-850K, HumanCytoSNP-12, HumanKaryomap-12 and the Infinium MethylationEPIC BeadChip. 

Scan time is approximately 40 minutes per BeadChip. Scan times can vary based on the number of samples and the type of BeadChip. For more information, see the data sheet NextSeq 550 Sequencing System.

Use the DMAP Decode File Client Utility to download the Decode File Client on a computer with access to the network location of the DMAP folder. The file client enables you to download DMAP files directly from Illumina servers using standard HTTP protocol.

No, because the BeadChip and flow cell use the same imaging components.

Run duration depends on the type of flow cell and number of cycles. For example run times, see the data sheet for the NextSeq 550 Sequencing System. Run duration is the same for the NextSeq 500 system and the NextSeq 550 system.

Local Run Manager run mode - No sample sheet is required.

Manual run mode - A sample sheet is required in the following cases:

• The system is configured for Run Monitoring and Storage in BaseSpace Sequence Hub. 
• When you use converted FASTQ files with a third-party analysis software. Use the Local Run Manager GenerateFASTQ software module to create a sample sheet. 

For NCS 2.2 or earlier, a sample sheet is only required when in standalone mode with converted FASTQ files and a third-party analysis software. Use Illumina Experiment Manager to create a sample sheet.

NextSeq 550 Systems running NCS v4 or later can use Local Run Manager software modules for on-instrument analysis. 

Additional analysis tools are available on BaseSpace Sequence Hub. You can also configure the NextSeq System to transfer data to a local server and perform analysis using third-party software.

If data transfer is interrupted during a run, data are stored temporarily on the instrument computer until the connection is restored. When the connection is restored, transferring of data resumes automatically.

If the connection is not restored before the end of the run, data must be removed from the instrument computer manually before a subsequent run can begin.