General Information

• Custom sequencing options: We support both custom primers and custom read lengths on our MiSeq, NextSeq500, and NextSeq2000 instruments. The number of basepairs listed in the tables below reflect the combined read length per flowcell (kit), and can be configured as single-end or paired-end reads of custom lengths. Contact us prior to placing an order to inquire about customizing your sequencing run.
• Quality checks: We will assess the concentration and size distribution of your Illumina samples and will ask you to approve the results before we continue with the sequencing run. If we observe any problems with sample quality (such as excess primers or adapter dimer peaks), we may recommend additional cleanup steps before sequencing (fees may apply). Samples that do not pass the quality checks will be charged for QC only if sequencing is cancelled.
• We are available to consult on Illumina sequencing options! Please use the ‘Ask a question’ button at the top of the page to send us an email, or sign up for office hours with an expert.

Instrument Information

The tables below for MiSeq, NextSeq500, and NextSeq2000 instruments show nominal read lengths. Different length runs can be performed on these sequencers, depending on the type of sample/indexing used. Sequencing runs on the NovaSeq instruments are standardized to 2x150bp paired-end reads, with limited options for index read lengths. Contact us prior to placing an order to discuss options. 
Sequencing output is shown for typical runs, but performance may vary, particularly for libraries with any regions of low complexity or for non-standard library types.
* Values represent the number of clusters sequenced; given for single-end reads. Ppaired-end mode would generates twice as many reads as single-end mode for the same number of clusters.
 

MiSeq

The MiSeq is a 4-color sequencer ideal for sequencing amplicons or other low complexity samples and for lower output projects. Low complexity pools will have lower data output due to increased % PhiX and lower loading density requirements. 

NextSeq 500/550

The NextSeq500 is a 2-color sequencer ideal for larger projects with complex libraries. The NextSeqs require the addition of higher amounts of PhiX to enable sequencing of libraries containing low-complexity inserts or read segments.

NextSeq 2000

The NextSeq2000 is a 2-color sequencer that uses a patterned flowcell and Illumina’s ExAmp clustering chemistry. Due to the higher frequency of ‘index hopping’ on patterned flowcells, we highly recommend the use of unique dual indices (UDIs) for sample barcoding on this instrument. The P3 flowcell currently offers the highest output on the NextSeq 2000.

Summer 2024: Illumina is releasing new flowcells with XLEAP chemistry and a new P4 flowcell with even higher output. Contact us for more information about new options on the NextSeq2000.

NovaSeq6000

The NovaSeq6000 is a 2-color sequencer that uses a patterned flowcell and Illumina’s ExAmp clustering chemistry. Due to the higher frequency of ‘index hopping’ on patterned flowcells, we highly recommend the use of unique dual indices (UDIs) for sample barcoding on this instrument. We offer sequencing lanes on the 4-lane S4 flowcell with 2 x 150bp paired end reads as the standard format on this instrument, with limited options for index read lengths. Other flowcells and sequencing read lengths may be available by special order and only for the entire flowcell (2-4 lanes); contact us for more information. 

NovaSeqX plus

The NovaSeqX is a 2-color sequencer that uses a patterned flowcell and Illumina’s new XLEAP chemistry. With XLEAP chemistry, the base that generates signal in both color channels is now ‘C’, which has implications for maintaining color balancing in the index reads. Due to the higher frequency of ‘index hopping’ on patterned flowcells, we highly recommend the use of unique dual indices (UDIs) for sample barcoding on this instrument. We offer sequencing lanes on the 10B and 25B 8-lane flowcells with 2 x 150bp paired end reads as the standard format on this instrument, with limited options for index read lengths. Other flowcells and sequencing read lengths may be available by special order and potentially only for the entire flowcell (8 lanes); contact us for more information.

Sample Preparation, Quality Control and Shipping

If the QC results for the samples indicate poor quality and sequencing is not recommended, we will not process your samples. You will be charged only for the QC, not the sequencing of samples that are likely to fail.

Illumina sample preparation and shipping