Products

Illumina Complete Long Reads product line

Revealing the most challenging regions of the genome

Illumina Complete Long Read sequencing technology enables highly accurate long and short reads on a single instrument

Front view of a female scientist holding a tube in one hand and single pipette in the other, preparing the flow cell for load.

Introducing Illumina Complete Long Read sequencing technology

This novel technology will bring more light to even the darkest corners of the genome. Illumina Complete Long Reads helps resolve the most challenging regions of the genome and makes long-read sequencing accessible and streamlined by enabling short and long reads from a single platform.

Illumina Complete Long Read technology powers a portfolio of novel, high-performance assays using standard next-generation sequencing (NGS) workflows and trusted Illumina sequencing by synthesis (SBS) chemistry.

Illumina Complete Long Read products

These kits offer optimized library prep and analysis performance for highly accurate, reliable results.

Key features and benefits

Accessible and cost-effective

Both long and short reads can be accessed using your existing Illumina sequencing system. Easily integrates into standard NGS workstreams without specialized equipment. Comprehensive, push-button cloud analysis available on BaseSpace Sequence Hub or Illumina Connected Analytics.

Robust and flexible

Low (50 ng) DNA input, tolerant to contaminants and freeze/thaw cycles. Generate contiguous long-read sequences with N50 of 5-7 kb with as low as 10 ng input DNA. Highly flexible long reads that can scale from small targeted panels up to long-read whole genomes.

Scalable and streamlined workflow

Simple, streamlined, and automation-friendly library prep without specialized equipment. Assay up to 3000 long-read whole genomes or tens of thousands of targeted long-read panels per year using NovaSeq X Series. Reduce batching requirements by assaying smaller sample numbers of targeted long reads using lower throughput consumables.

Highly accurate

Powered by proven Illumina SBS and DRAGEN analysis on BaseSpace Sequence Hub or Connected Analytics. Capable of F1 score (SNVs + indels) of 99.90% for human whole genomes as measured by PrecisionFDA Truth Challenge v21 and enabling phased sequencing of regions > 100 kb.

How Illumina Complete Long Read technology works

Tagmentation is used to normalize long fragment sizes. Long fragments are “land-marked” to capture single-molecule, long-read information and amplified. Marked fragments are tagmented to standard libraries for sequencing. Marked and unmarked data are combined to generate highly accurate complete long reads.

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Long-read sequencing

Long- and short-read data

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A new standard for accuracy

Illumina Complete Long Read Prep, Human delivers unprecedented accuracy for variant calling with PrecisionFDA Truth Challenge v2 data sets,1 as measured by F1 score (%), a calculation of true positive and true negative results as a proportion of total results.

  • Improves upon the exceptional, award-winning accuracy of Illumina SBS + DRAGEN analysis1-3
  • Can be used to augment existing WGS data sets or as a reflex tool for deeper variant discovery
  • Delivers highly accurate, reliable results across samples of variable quality

Illumina Complete Long Reads and PrecisionFDA Truth Challenge v2 data sets

Illumina Complete Long Reads webinar

In this presentation, we share use cases of Complete Long Reads and highlight research being done by collaborators around the world.

View webinar

Illumina Complete Long Reads WGS workflow

1
Extract

Extract DNA from blood or saliva with no specialized protocols, no shearing, and no size selection required.

2
Prep
3
Sequence
4
Analyze

Supporting data

Clear haplotype assignment

Illumina Complete Long Reads can resolve highly polymorphic regions like the HLA-A gene. Uniform coverage in the HLA region enables accurate phasing of HLA alleles.

Detection of large deletions

A heterozygous 180 bp deletion in the SEMG1 gene is clearly detected by both Illumina Complete Long Reads and on-market long reads.

Resolution of STRC from its pseudogene

Both Illumina Complete Long Reads and on-market long reads clearly resolve the 23 kb STRC gene from its pseudogene, pSTRC.

Enhanced coverage in challenging regions of protein-coding genes

Low-coverage regions in the RHCE gene are resolved using Illumina Complete Long Read Prep with Enrichment and the Human Comprehensive Panel.

High-quality performance across a wide range of DNA inputs

Illumina Complete Long Read Prep, Human with 5 ng to 1200 ng input DNA (in triplicate) generates similar data quality for N50 and phase block N50. N50 is the sequence length of the shortest contig (or phase block) at 50% of the total assembly length.

Human phasing

Perform phased sequencing with Illumina Complete Long Reads to identify co-inherited alleles, haplotype information, and phase de novo mutations.

Close up and blurry image of the back side of a male scientist examining a second 25B flow cell cartridge before inserting into a NovaSeq X drawer.

Compatible with high-throughput Illumina sequencers

Illumina Complete Long Read technology is compatible with the NovaSeq X Plus, NovaSeq X, and NovaSeq 6000 Sequencing Systems, giving you access to both long- and short-read data on the same instrument.

View sequencers

Additional resources

Illumina Long Read technology benefits

This recorded presentation from our ASHG 2022 CoLab talk describes the benefits of our novel long-read technology and how it is complemented by other technical innovations in our roadmap.

Speak to a specialist

Learn how your lab can benefit from the accuracy and scalability of our long-read technology.

References
  1. Truth Challenge V2: Calling Variants from Short and Long Reads in Difficult-to-Map Regions. Precision FDA website. precision.fda.gov/challenges/10. Accessed March 3, 2025.
  2.  Mehio R, Ruehle M, Catreux S, et al. DRAGEN Wins at PrecisionFDA Truth Challenge V2 Showcase Accuracy Gains from Alt-aware Mapping and Graph Reference Genomes. Illumina website. illumina.com/science/genomics-research/articles/dragen-wins-precisionfda-challenge-accuracy-gains.html. Accessed March 3, 2025.
  3. Illumina. Accuracy improvements in germline small variant calling with the DRAGEN Bio-IT Platform. illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/dragen-v4-accuracy-app-note-m-gl-01016/dragen-v4-accuracy-app-note-m-gl-01016.pdf. Published 2025. Accessed March 3, 2025.