Illumina Sequencing Only

Ready to sequence your Illumina libraries? We've got you covered!

We have a variety of services to accommodate your Illumina sequencing needs from 1M reads to 25B reads in a single run. Options include purchasing an entire MiSeq, NextSeq, or NovaSeq X flowcell, NovaSeq lane, or 100M read fraction of a NovaSeq lane to meet your specific sequencing needs. Pool your own libraries or take advantage of our QC and pooling services.

Turnaround time is ~1 week (may vary according to volume of samples, flowcell inventory)

To get started, please read the requirements carefully and don't hesitate to contact us if you have any questions.

Requirements Summary

Concentration: 4nM per library or pool (we can sometimes work with less)
Volume: 30ul (10ul minimum)
Indexing: Unique Dual Indexes are required for 100M read NovaSeq X sequencing.

Please see SAMPLE SUBMISSION for more information.

Concentration

We recommend submitting 30 µL of a 4 nM library pool per full lane, which yields approximately 1.2 billion reads (12 × 100 million reads). For any order, please provide at least 10 µL of 4 nM library. If you have less material, that’s fine—we can usually work with lower volumes or concentrations. The recommended amount gives us flexibility for QC and possible reprocessing, but it is a guideline rather than a strict requirement. You’re also welcome to submit more if available.
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The most helpful step you can take is to include any relevant QC data in your iLab submission. If your pool is below the recommended volume or concentration (<10 µL or <4 nM), just note it in iLab. We are experienced in handling low-input samples and often generate high-quality data even under challenging conditions.

Unique Dual Indexes

• Index Hopping is a sequencing artifact where sample index sequences are incorrectly reassigned to different library fragments during sequencing, leading to misattribution of reads between samples.​ Unique Dual Indexes prevent index hopping contamination, and are a requirement for NovaSeq X Plus sequencing. ​​More on index hopping:
  • Illumina Index Hopping White Paper
  • Illumina Website regarding index hopping (and mitigation)
• Recommended UDI products
  • ​NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs)
• Single index – whole lane only
  • If your experimental goals require single indexes, we can still assist in generating data. You will need to purchase entire lanes or flowcells understanding that you may be susceptible to ~1% cross sample contamination due to index hopping. Please contact us to determine the most appropriate sequencing strategy. 

Adapter Dimers

Adapter dimers are small typically 130-150bp artifacts formed during NGS library preparation when sequencing adapters ligate to each other rather than to DNA fragments. These dimers can be preferentially amplified and sequenced, wasting reads and reducing the overall quality and yield of usable data.

Illumina recommends an adapter dimer percent <0.5% for loading NovaSeq X patterned flowcells (ref), however can work with dimer that are <5%, if only present in a few of the multiplexed libraries.

When potentially problematic dimers are detected during our pre-sequencing QC, MBCF staff will reach out to discuss your options and make recommendations.
 

QC & Pooling Services

You can do it....or MBCF can do it

MBCF quality control assays include concentration measurement by qubit fluorometer, fragment size characterization by TapeStation, and either light Illumina sequencing on the MiSeq, or qPCR (for pre-pooled full lane/flowcell requests)

Pre-pooled Libraries (you pooled them):

As a general rule, we recommend not pooling different application types before sequencing, since pooling libraries of the same type carries fewer risks. Submitting separate requests for each application allows us to group similar libraries together and optimize sequencing performance.

We have extensive experience pooling diverse library types and can often determine which combinations work well. For example, while ATAC libraries can be challenging, we routinely pool them with Cut&Run and ChIP libraries. In contrast, pooling CRISPR and 10X libraries is more difficult, as they often require very different loading concentrations.

If you would like to pool different library types in your own lab, we recommend discussing with us first. In most cases, we’ve handled similar pooling scenarios before—and if not, we’re always glad to experiment and collaborate.
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Unpooled Libraries (MBCF will pool them):

MBCF makes an initial pool based on molar concentration estimates using qubit and tapeStation data followed up by light sequencing. If needed, pools are re-balanced based on the light sequencing data prior to deep sequencing on the NovaSeq X.

If we perform the pooling for you, you gain an extra layer of quality assurance: should any of your libraries not meet minimum read requirements, we will provide additional sequencing at no extra charge.

How to choose? 100M reads, Lane, or Flowcell

You can purchase multiple 100M read chunks. If you need >700M reads, you should consider upgrading to a full lane — more data at a lower price.

We offer three sequencing‑only options on the NovaSeq X Plus: 100 M read blocks, single lanes, and full flow cells. The right choice depends on your project’s size and desired sequencing depth.

• 100 M read blocks – Best for smaller projects or pilot studies. Can be ordered in any block of whole numbers.
   
• Single lane (10B flow cell) – Suitable when you need ~1.2 billion paired‑end reads (or >700M reads). 
   
• Full flow cell (10B or 25B) – Recommended when you require maximum data output or need custom primers. A full 25B flow cell provides ~25 billion paired‑end reads, which can be partitioned among multiple libraries in your own pool. This option offers the lowest per‑base cost but is generally reserved for very large projects.
   

If you are unsure which option matches your experimental goals, please feel free to reach out. We can help estimate the number of reads required based on project and applications specific requirements and help you select the most appropriate and cost-effective option.

Custom Sequencing Primers (Advanced)

For advanced sequencing library prep designs, it is possible to use custom sequencing primers. However, before moving forward with a project that might require this type of customization, please consult with us.

In order to support custom sequencing primers, you must purchase a whole flowcell from any of our available sequencing platforms. For NovaSeq X Plus, the lowest throughput flowcell generates 1.5B reads.