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URMC / Research / Rochester Genomics Center / Instrumentation / Sequencing Instruments

 

GRC Sequencing Instrumentation

New Addition: Illumina NovaSeq X Plus Sequencer

Learn more about the NovaSeq X system

NovaSeq X PLUS NovaSeqXPlus Run Recipe Chart

The NovaSeq X has patterned flow cell technology and it is highly recommended that samples utilize the Unique Dual Indexing strategy to minimize the risk of index hopping

NovaSeq X Performance Specifications

NovaSeq Applications:

  • Whole Genome Sequencing
  • Whole Exome Sequencing
  • Whole Transcriptome Sequencing

Illumina NovaSeq 6000 Sequencer

Learn more about the NovaSeq6000 system 

NovaSeq Instrument ImageNovaseq Flow Cells and Run Recipes

The NovaSeq 6000 has patterned flow cell technology and it is highly recommended that samples utilize the Unique Dual Indexing strategy to minimize the risk of index hopping

NovaSeq 6000 Performance Specifications

NovaSeq Applications:

  • Whole Genome Sequencing
  • Whole Exome Sequencing
  • Whole Transcriptome Sequencing

New Addition: Illumina NextSeq 2000

Learn more about the NextSeq 2000 System

NextSeq 2000 Instrument Image

 

NextSeq 2000 flow cell options with available run recipes

 

The NextSeq 2000 is the latest addition to sequencing instruments at the GRC. This instrument will replace the NextSeq 550 (Jan 1, 2024) and provide researchers with greater flexibility, faster run times, and lower sequencing costs. 

The NextSeq 2000 has patterned flow cell technology and it is highly recommended that samples utilize the Unique Dual Indexing strategy to minimize the risk of index hopping

NextSeq 2000 Performance Specifications 

NextSeq 2000 Applications:

  • Exome Sequencing
  • Whole Transcriptome Sequencing
  • Small Whole Genome Sequencing
  • Epigenetic Sequencing 

Illumina NextSeq 550 (Sunset: January 1, 2024)

Learn more about the NextSeq 550 System 

NextSeq Instrument ImageNextSeq 550 flow cell options with available run recipes

NextSeq 550 Performance Specifications

NextSeq 550 Applications:

  • Gene Expression Profiling
  • Exome Sequencing
  • Whole Genome Sequencing

Announcement regarding sunset of NextSeq 550 (January 1, 2024)

As of January 1, 2024, we will no longer be sequencing with the NextSeq 550. This platform has been used for projects that have not yet incorporated the Unique Dual Indexing (UDI) strategy. If your lab needs assistance with modification of lab protocols to incorporate UDIs, please contact us for assistance. Projects that utilize alternative indexing strategies (i.e. single index or combinatorial dual) can still be sequenced on all platforms with the understanding that index hopping may occur. 

Illumina MiSeq 

Learn more about the MiSeq System

MiSeq InstrumentMiSeq flow cells

MiSeq performance specifications

MiSeq Applications:

  • Amplicon Sequencing
    • 16s (microbiome)
    • Targeted/Custom Panels
      • Rep-seq
      • Targeted Amplicon Panels
        • TruSeq Cancer Amplicon (LINK)
        • TruSight Myeloid Panel (LINK)
  • Small Genome Sequencing
    • Bacteria, Viruses, etc.

Recommended Reads Per Library:

Application Reads per Library
mRNA-Seq 20 - 25 Million
Total RNA-Seq 40 - 50 Million
Small RNA-Seq 2 Million
Low Input RNA-Seq 20 - 25 Million
Chip-Seq 15 Million
ATAC-Seq 50 Million
Whole Genome (10X) 125 Million Pairs
Whole Genome (4X) 50 Million Pairs
Whole Genome Bisulfite-Seq (10X) 125 Million Pairs
Whole Exome Sequencing (100X) 50 Million Pairs
Single Cell (10X v3) 100,000 per Cell

 

**The above recommendations are based on Human/Mouse/Rat genomes for simplicity and empirical results from GRC experience.  Other organisms may require different sequencing depths (more or less samples per lane).  The amount of sequencing performed and the type (single vs pair) is organism and application specific.  These recommendations are guidelines and by no means meant to be strict cutoffs.  Internal GRC data and cumulative data analysis over the past formed the basis for these suggestions with the sole purpose to help investigators select the most appropriate experiment type for their research goals.

 

NovaSeq, NextSeq, and MiSeq Flow Cell Image

Contact us or use the Sequencing Platform Comparison Tool to find the right alternative for your research needs. 

Data Analysis

The GRC has an experienced group of bioinformatics staff with experience in NGS data analysis methods and workflows.  For more information please visit the GRC Bioinformatics Page or contact us.