Illumina Full Flowcell Runs

This service is designed for customers intending to prepare sequencing-ready libraries themselves and submit the final pooled libraries for sequencing on one of our Illumina instruments. Demultiplexing of your run is provided at no additional charge when you provide your barcode sample sheet. No library preparation service is included with these offerings.

For dedicated flowcell runs, the platform and flowcell set the total maximum number of reads produced, and the kit and cycle number dictate the maximum read length. For example, a 100-cycle kit can produce 100 bp single end reads or 2×50 bp paired end reads. Customers also need to account for any PhiX being added when judging if total read output will produce the desired amount of on-target data. (See below for additional details on PhiX.)

Interested in a flowcell and kit not listed here? We are happy to provide quotes for any of Illumina’s current reagent kits for our machines. However, for projects of all sizes that require 300-cycle kits, our dedicated NovaSeq X lanes are a fantastic option with the introduction of the NovaSeq X Plus. The incredible price point means that upgrading to an X Plus lane from a NextSeq 2000 or NovaSeq 6000 option often costs less and delivers more data.

Requirements for ALL Pooled Libraries:

  • Single pool of libraries with total volume of 30µL or more (pooling service is not provided)
  • Final pool concentration greater than 1ng/uL

For NovaSeq X 10B Lanes ONLY:

Please provide the following run specifications in the order notes for your prepared library:

  • Index Structure:
    • Single or dual indices
    • Index length (maximum of 10bp)
  • Loading concentration (in pM)
  • Expected total fragment size (insert + adapters)
  • (Optional) PhiX spike-in percentage
  • (Optional) Demultiplexing key

What You Will Receive:

  • Complete Illumina sequencing output, including log and report files
  • If a demultiplexing key with sample names was provided, fastq files for individual samples
  • Data shared via Box folder within 2 weeks

For all Other Dedicated Full Runs/Flowcells:

Please provide the following run specifications in the order notes for your prepared library:

  • Read Structure:
    • Read length (should agree with the number of cycles)
    • Paired end (PE) or Single end (SE)
  • Index Structure:
    • Single or dual indices
    • Index length (maximum of 10bp)
  • Loading concentration (in pM)
  • Expected total fragment size (insert + adapters)
  • (Optional) PhiX spike-in percentage
  • (Optional) Demultiplexing key
  • If applicable, custom primers must be supplied

MiSeq Flowcells

Sequencing Package
(Minimum Read Count Per Sample)
Price*
300cyc Nano v2 (1M SE Reads or 2M PE Reads)
300Mbp of Data
$615.00
500cyc Nano v2 (1M SE Reads or 2M PE Reads)
1.2Gbp of Data
$705.00
300cyc Micro v2 (4M SE Reads or 8M PE Reads)
300Mbp of Data
$755.00
300cyc v2 (12.5M SE Reads or 25M PE Reads)
4.8Gbp of Data
$1,650.00
500cyc v2 (12.5M SE Reads or 25M PE Reads)
8Gbp of Data
$1,900.00
600cyc v3 (25M SE Reads or 50M PE Reads)
15Gbp of Data
$2,500.00
*Orders >48 Samples receive 5% discount

NextSeq 2000 Flowcells

Sequencing Package
(Minimum Read Count Per Sample)
Price*
P1 100cyc (100M SE Reads or 200M PE Reads)
10Gbp of Data
$1,400.00
P1 600cyc (100M SE Reads or 200M PE Reads)
60Gbp of Data
$3,300.00
P2 100cyc (400M SE Reads or 800M PE Reads)
40Gbp of Data
$2,150.00
P2 600cyc (300M SE Reads or 600M PE Reads)
180Gbp of Data
$6,200.00
P3 50cyc (1.2B SE Reads or 2.4B PE Reads)
60Gbp of Data
$3,200.00
P3 100cyc (1.2B SE Reads or 2.4B PE Reads)
120Gbp of Data
$4,700.00
*Orders >48 Samples receive 5% discount

NovaSeq X Plus Flowcells

Sequencing Package
(Minimum Read Count Per Sample)
Price*
1.5B 300cyc (1.5B SE Reads or 3B PE Reads)
450Gbp of Data
$4,000.00
10B 100cyc (10B SE Reads or 20B PE Reads)
1Tbp of Data
$9,500.00
10B 200cyc (10B SE Reads or 20B PE Reads)
2Tbp of Data
$11,800.00
10B 300cyc (10B SE Reads or 20B PE Reads)
3Tbp of Data
$12,000.00
25B 300cyc (25B SE Reads or 50B PE Reads)
8Tbp of Data
$22,500.00
1 Lane 10B 300cyc (2.5B 151bp PE Reads)
375Gbp of Data
$1,520.00
*Orders >48 Samples receive 5% discount

Increasing Library Diversity and Success with PhiX

Customers must consider if PhiX is needed to successfully sequence a low-diversity library and, if used, may need to adjust their chosen flowcell size. A sequencing library is considered low-diversity when any portion of the library fragments are identical for a majority of the combined pool, which is common for amplicon or Tn-Seq libraries. This stretch of shared sequence causes optical errors for Illumina machines and can result in decreased output or outright failure. Added as a relative percentage, a PhiX spike-in adds prepared phage library to increase diversity and enable processing, but a proportional amount of the final data will be off-target PhiX sequences.

Recommended PhiX percentages depend on library construction type and sequencing platform. When using a library preparation kit, we recommend consulting the manufacturer’s documentation. Illumina’s fantastic technical support team can also provide guidance for custom libraries.

Go to Top