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Illumina Complete Long Read Prep, Human

Highly accurate, high-performance full workflow solution for comprehensive human WGS with long-read data from NovaSeq platforms.

~7.5–8.5 hr

Assay time

5–6 hr including (PCR and QC)

Hands-on time

50 ng DNA recommended

Input quantity

See full details in the specifications table

Overview

With Illumina Complete Long Read technology, long-read sequencing is now accessible and streamlined for genomic labs. Illumina Complete Long Read Prep, Human is the first product to utilize this technology, providing the most comprehensive view of the genome. The high-performance whole-genome sequencing assay uses a standard NGS workflow to generate contiguous long-read sequences on the NovaSeq 6000 System and NovaSeq X Series.

  • Streamlined, accessible assay with long and short reads on a single platform, compatible wth the NovaSeq X Series and NovaSeq 6000 System

  • Optimized standard NGS library prep and DRAGEN secondary analysis for highly accurate, reliable results

  • Robust and flexible performance with low input requirements, no specialized extraction, shearing, or size selection required

  • Efficient, single-day, automation-friendly workflow that is more scalable than on-market long-read solutions

  • Note: Analysis requires standard, ≥30× short-read WGS data from the same sample.

Highly accurate, scalable assay

Illumina Complete Long Read data complements standard short-read WGS data and delivers more comprehensive whole genomes by:

  • Calling variants in challenging, challenging-to-map regions with high homology or repetitive regions
  • Resolving complex structural variants, pseudogenes, and large insertion–deletions (indels)
  • Phasing variants and calling haplotypes

Learn more about Illumina Complete Long Read technology

Specifications

Assay time ~7.5–8.5 hr
Automation capability Liquid handling robot(s)
Description Illumina Complete Long Read Prep, Human performs long-read human germline whole-genome sequencing using existing Illumina NovaSeq platforms.
Hands-on time 5–6 hr including (PCR and QC)
Input quantity 50 ng DNA recommended
Instruments NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System, NovaSeq X Plus System
Mechanism of action Bead-linked transposome, land-mark reads
Method Long-read sequencing, Whole-genome sequencing
Multiplexing Up to 48
Nucleic acid type DNA
Number of reactions 8 or 24
Sample type details DNA extracted from blood or saliva
Specialized sample types Blood, Not FFPE-compatible, Low-input samples, Saliva
Species category Human
Target insert size 500–700 bp
Technology Sequencing
Variant class Short tandem repeats (STRs), Germline variants, Structural variants, Single nucleotide variants (SNVs), Insertions-deletions (indels)

Required products

llumina Complete Long Read Prep, Human includes the required analysis package.
Choose the sequencing reagents appropriate for your instrument. 
Index adapters are optional and sold separately.
Illumina Complete Long Read DRAGEN Cloud Analysis.
BaseSpace Sequence Hub Professional or Enterprise subscription required.
iCredits for storage (optional).

/ Results

Applications

Example workflow

1
Prep

Illumina Complete Long Read Prep, Human

2
Sequence*
3
Analyze

* Sequencing Illumina Complete Long Read libraries on NovaSeq platforms may cause the reported Q30 score of a run to fall below the NovaSeq specification. This does not indicate a performance issue with the sequencing run, nor the library.

Project recommendations

Instrument Recommended number of samples Read length
NovaSeq 6000 System

4 samples (1 sample per lane of an S4 flow cell).
8 samples (1 sample per lane of an S4 flow cell, dual flow cell run optional).
A paired PCR-free WGS library is required for analysis (Illumina DNA PCR-Free Prep recommended).
NovaSeq 6000 Xp Workflow kit.

2 × 150 bp

NovaSeq X System

4 samples (1 sample per 2 lanes of a 10B flow cell).
A paired PCR-free WGS library is required for analysis (Illumina DNA PCR-Free Prep recommended).
11 samples (25B flow cell).

2 × 150 bp

NovaSeq X Plus System

8 samples (1 sample per 2 lanes of a 10B flow cell, dual flow cell run).
A paired PCR-free WGS library is required for analysis (Illumina DNA PCR-Free Prep recommended).
22 samples (25B flow cell, dual flow cell run).

2 × 150 bp

NovaSeq 6000Dx in Research Mode

4 samples (1 sample per lane of an S4 flow cell).
8 samples (1 sample per lane of an S4 flow cell, dual flow cell run optional).
A paired PCR-free WGS library is required for analysis (Illumina DNA PCR-Free Prep recommended).
NovaSeq 6000 Xp Workflow kit.

2 × 150 bp

Related applications and methods

Rare disease whole-genome sequencing

Whole-genome sequencing is the most comprehensive test for rare disease, with the potential for superior diagnostics and outcomes.

Whole-genome sequencing

Whole-genome sequencing delivers a comprehensive view, ideal for discovery applications. Newer genome sequencers perform WGS more rapidly than ever.

Genetic and rare diseases

NGS technology is helping to drive breakthroughs in genetic disease testing by facilitating early detection and diagnosis.

Documentation

Product literature
Support documentation

Figures

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. Learn more about Illumina Complete Long Read technology.

Long-read phased sequencing enables 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.

Long-read sequencing can detect 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.

Long-read sequencing can resolve pseudogenes

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

Long-read sequencing can identify STR insertions

Insertions in short tandem repeat (STR) regions are clearly detected by both Illumina Complete Long Reads and on-market long reads.

Long-read sequencing can resolve pseudogenes

Both Illumina Complete Long Reads and on-market long reads clearly resolve the SULT1A1 gene (a pharmacogenomic marker) from its pseudogene, SULT1A2.

High-quality performance across a wide range of DNA input

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

Resources

Thumbnail

Introducing Illumina Complete Long Reads

Illumina Complete Long Reads can help resolve the most challenging regions of the genome and make long-read sequencing accessible by enabling short and long reads from a single platform.

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.

Illumina Complete Long Read technology: Detailed insights into complex genomes

Illumina Complete Long Read technology can help accelerate access to the remaining ~5% of genic regions. Hear Andrew Shaver, Product Manager describe the benefits of the Illumina novel long-read technology, including the accuracy, scalability, and workflow benefits. 

Illumina Complete Long Read Prep, Human (24 samples)

20089108

This reagent kit contains necessary reagents to support the preparation of 24 libraries for Illumina Complete Long Read Prep workflow. Index adaptors must be purchased separately. iCredits must be purchased for analysis.

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Illumina Complete Long Read Prep, Human (8 samples)

20086823

This reagent kit contains necessary reagents to support the preparation of 8 libraries for Illumina Complete Long Read Prep workflow. Index adaptors must be purchased separately. iCredits must be purchased for analysis.

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Illumina® Unique Dual Indexes, LT (48 Indexes, 48 Samples)

20098166

Illumina® Unique Dual Indexes, LT (48 Indexes, 48 Samples)

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Illumina Complete Long Read Prep, Human-24, S4 Starter Pack

20099754

This package contains 1 ICLR-24 sample kit, 6 NovaSeq 6000 S4 (300) cyc kits, and 6 NovaSeq XP-4 lane kits.

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Illumina Complete Long Read Prep, Human-24, 10B Starter Pack

20099755

This package contains 1 ICLR-24 sample kit, 6 NovaSeq X 10B (300) cyc kits.

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