General Information

• Selecting an Illumina instrument and sequencing kit to fit your project needs: there are important differences in read lengths, output, sequencing chemistry, and ability to customize the run. See below for technical details about each Illumina instrument and run type.
• 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. Typical yields (Reads passing filter* values) represent the number of clusters sequenced; given for single-end (SE) reads. Paired-end (PE) mode generates twice as many reads as single-end mode for the same number of clusters.
• Custom sequencing options: We support both custom primers and custom read lengths on the 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. Sequencing runs on the NovaSeq instruments are standardized to 2x150bp paired-end (PE) reads, with limited options for index read lengths and no custom sequencing primers. Contact us prior to placing an order to discuss options.
• Sequencing chemistry: Illumina’s new XLEAP chemistry used on the 2-color NovaSeqX and NextSeq2000 instruments has important implications for color balancing of the index reads, especially for sequencing runs containing a small number of libraries (low diversity index reads). Each position in the index read should generate signal in both channels to minimize issues with sequencing quality. With XLEAP chemistry, ‘C’ is the dual color nucleotide that generates signal in both channels; with Illumina’s older standard Sequencing By Synthesis (SBS) chemistry used on the NextSeq500 (and optionally the NextSeq2000), ‘A’ is the dual color nucleotide. ‘G’ generates no signal for both chemistries, and the other 2 bases generate signal in 1 channel. If you use an instrument+flowcell with XLEAP chemistry, please plan for this change in index color balancing when barcoding your libraries. (Note that the miSeq is a 4-color sequencer and index color balancing is rarely a concern.)
• 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

NovaSeq instruments

The NovaSeqX is a 2-color sequencer that uses a patterned flowcell and Illumina’s new XLEAP 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 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. New: for projects requiring less than a full lane of sequencing, we now support lane sharing on the NovaSeq platform (2x150nt PE reads, max 10nt index read lengths, UDIs required). 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. We can also provide sequencing options on the older NovaSeq6000 instrument (standard SBS chemistry), either individual lanes on the P4 flowcell (2x150nt PE reads) or full flowcells (2-4 lanes) with custom read lengths by special order.

NextSeq 2000

The NextSeq2000 is a 2-color sequencer that uses a patterned flowcell and Illumina’s standard SBS 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. Flowcells are now available for both XLEAP and standard SBS chemistry; XLEAP flowcells are often less expensive than standard SBS. See above for notes on differences in index color balancing between XLEAP and standard SBS. The new P4 flowcell (XLEAP chemistry only) offers the highest output on the NextSeq 2000.

NextSeq 500/550

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

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. Contact us to consult on optimizing amplicon sequencing to improve data quality and output. 

Illumina sample preparation and shipping