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 to load
  • (Optional) Demultiplexing key, sent in response to order confirmation

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 to load
  • (Optional) Demultiplexing key, sent in response to order confirmation
  • If applicable, custom primer aliquots 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
*Orders >48 Samples receive 5% discount

NovaSeq X Plus Flowcells

Sequencing Package
(Minimum Read Count Per Sample)		 Price*
1.5B 100cyc (1.5B SE Reads or 3B PE Reads)
150Gbp of Data		 $3,100.00
1.5B 200cyc (1.5B SE Reads or 3B PE Reads)
300Gbp of Data		 $3,800.00
1.5B 300cyc (1.5B SE Reads or 3B PE Reads)
450Gbp of Data		 $4,200.00
10B 100cyc (10B SE Reads or 20B PE Reads)
1Tbp of Data		 $9,400.00
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		 $21,500.00
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.

Contact:
91 43rd Street, Ste. 250
Pittsburgh, PA 15201
(878) 227-4915

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Full Flowcell:

We offer full flowcell sequencing services for libraries that have been prepared outside of our lab. For each library, we will need to know the loading concentration, phiX spike-in, and run structure. Data is delivered as a complete run folder and can be demultiplexed upon request if a sample sheet is provided.

SARS-CoV-2 Sequencing:

Our SARS-CoV-2 Sequencing services include an assembly on the SARS-CoV-2 reference genome as a scaffold. These packages provide roughly 200Mbp of paired end reads (2×151 bp) as fastq files and the assembly in fasta format.

We require a minimum sample volume of 15 µL of extracted material (or 250µL for VTM samples) and recommend that only samples with Ct values below 35 are sent (because submissions are not measured for viral load before processing). We offer services for both purified RNA and samples in VTM media that require viral RNA extraction. Please see our SARS-CoV-2 Sequencing page for more detailed information.

Microbiome Sequencing:

Please see our Microbiome Sequencing page for package details, including distributables and sample requirements.

Nanopore Sequencing:

Our Oxford Nanopore sequencing packages provide reads equal to the length of input DNA, delivered as a fastq file.

For each sample, we require a minimum volume of 60 µL, and at least 40 ng/µL dsDNA quantified by Qubit or other dye-based method (100 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Long Read Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

PacBio:

Our PacBio services deliver HiFi reads with an average read length of 8-12kb for standard offerings and up to 25kb for full flowcell runs. All package names are listed by the minimum number of >Q20 reads that will be delivered. Both assembly and annotation are included with all packages.

For each sample, a minimum volume of 60 µL and at least 35 ng/µL dsDNA (quantified by Qubit or other dye-based methods) are required. SeqCenter strongly recommends utilizing our HMW DNA Extraction service for best results; however, we will also accept samples that are shipped on dry ice to avoid DNA integrity issues caused by the shipping process.

Please see our PacBio Sequencing page for more detailed information about our services.

RNA Sequencing:

We offer both rRNA depletion RNA squencing and polyA-tail enrichment mRNA sequencing. Both provide stranded, paired end reads (2x 151bp) as fastq files.

For each sample, we require a minimum volume of 20µL and at least 50ng/µL RNA. We also recommend, but do not require, that samples be DNAse treated and have a RIN score greater than 6. We also offer Basic and Intermediate RNAseq analyses, which require an annotated reference sequence.

Please see our RNA Sequencing page for more detailed information about both our RNA sequencing and analysis packages.

Illumina Sequencing:

The Illumina sequencing packages produce paired end reads (2×151 bp) delivered as fastq files.

For each sample, we require a minimum volume of 30 µL and at least 10 ng/µL dsDNA quantified by Qubit or other dye-based method (20 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Whole Genome Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

For additional information about variant calling and short read assemblies, please see our Bioinformatics page.

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