Illumina Sequencing

_________________________________________________________

JUMP TO TOPIC:

__________________________________________________________

ILLUMINA SERVICES OVERVIEW

The GC3F began offering Illumina sequencing services in the early days of next-generation DNA sequencing in 2008.  Since then, we have sequenced literally thousands of samples on multiple Illumina platforms.  We played a significant role in the development of the RAD-seq technique that was invented at UO, and are still happy to sequence “unconventional” libraries on our instruments.

The GC3F currently operates three Illumina DNA sequencers:

  • MiSeq
  • NovaSeq 6000
  • NextSeq 2000

Prices for all run types are listed at the bottom of this page.

BACK TO TOP

__________________________________________________________

Illumina NovaSeq 6000 Sequencing 

 Thanks to a generous award from the Murdock Charitable Trust, GC3F is now offering Illumina sequencing services on a NovaSeq 6000 sequencer. The NovaSeq will be taking the place of our workhorse HiSeq 4000, and offerings the following advantages over the older platform:

  • Multiple output modes from 400M up to 2500M read pairs per lane
  • Lower cost per Gbp than HiSeq 4000, even in the lowest NovaSeq output mode (SP)
  • Low cost per Gbp in high output (S4) mode
  • Fewer lanes per flowcell = less lead time waiting for lane submissions from other users needed to launch runs
  • Full compatibility with all Illumina library types

Log in to iLab to submit a sample to run on the NovaSeq!

Pricing info for single-lane NovaSeq sequencing

Run Type

Internal Rate

External Rate

Run Configurations

Read Pairs per lane**
S4 300 Cycle $4,444 $5,778 PE 2x150 2-2.5 billion+
S4 35 Cycle $3,416 $4,442 SR 53*, PE 2x32* 2-2.5 billion+
         
S1 300 Cycle $3,416 $4,440 PE 2x150 650-800 million+
S1 100 Cycle $2,555 $3,322 SR 118*, PE 2x59* 10X scRNA 650-800 million+
         
SP 500 Cycle $2,792 $3,630 PE 2x250 325-400 million+
SP 300 Cycle $2,032 $2,643 PE 2x150 325-400 million+
SP 100 Cycle $1,475 $1,917 SR 118*, PE 2x59* 10X scRNA 325-400 million+

*All NovaSeq kits contain sufficient reagent to sequence an additional 38nt beyond the specified cycle number (SP 100 cycle kits contain reagents for 138 cycles, S4 35 cycle kits contain reagnets for 73 cycles, etc). These can be used for 10X cell barcodes, long dual index reads, or extended read length for the library inserts

**These are the official Illumina output specs and are conservative. Real world performance will often exceed these read numbers

BACK TO TOP

__________________________________________________________

 

Illumina MiSeq Sequencing 

 

The Illumina MiSeq is a benchtop instrument designed for lower-output sequencing applications such as amplicons (targeted resequencing), small genomes, miRNA & small RNA, and targeted gene expression profiling.

In addition to offering both single read (SR) and paired end (PE) read types, it can be operated in 4 different output modes to help you narrow in on the ideal configuration for your experiment:

  • v3 mode:  Up to 25M reads at max read length of 300bp
  • v2 mode:  Up to 15M reads at max read length of 250bp
  • Micro mode:  Up to 4M reads at max read length of 150bp
  • Nano mode:  Up to 1M reads at max read length of 250bp

Please submit 25 µL minimum volume of your MiSeq libraries at 2-20 nM concentration in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable).  

CLICK HERE to submit a MiSeq sequencing request! (Note, you will need to register for an iLab account.)|
 

Run Type

Internal Rate

External Rate

Run Configurations

Read Pairs per lane
v3 600 cycle $1,786 $2,635 PE 2x300 ~22-25 million
v3 150 cycle $1,084 $1,599 SR 150, PE 2x75 ~22-25 million
v2 500 cycle $1,375 $2,029 PE 2x250 ~12-15 million
v2 50 cycle $978 $1,442 SR 50 ~12-15 million
v2 micro, 300 cycle $565 $834 PE 2x150 ~4 million
v2 nano, 500 cycle $469 $692 PE 2x250 ~1 million
v2 nano, 300 cycle $405 $598 PE 2x150 ~1 million

BACK TO TOP

__________________________________________________________

NextSeq 2000 Sequencing

nextseq_2000

The NextSeq 2000 is the latest medium output sequencer from Illumina. There are currently 3 output modes available.

  • P3 flowcells yield ~1.2 billion read pairs
  • P2 flowcells yield ~400 million read pairs
  • P1 flowcells yield ~100 million read pairs

One user-submitted library is loaded per run, so there is never any waiting for additional libraries to arrive in the facility to fill flowcells.  Read length options are slightly different, but NextSeq flowcells are 100% compatible with libraries generated for other Illumina sequencing instruments.  

Please submit 25 µL minimum volume of your NextSeq libraries at 2-20 nM concentration in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable).

CLICK HERE to submit a NextSeq 2000 sequencing request! (Note, you will need to register for an iLab account.)
 

Run Type

Internal Rate

External Rate

Run Configurations

Read Pairs per lane
P3 300 cycle $4,190 $5,447 PE 2x150 up to 1.2 billion
P3 200 cycle $3,267 $4,247 PE 2x100 up to 1.2 billion
P3 100 cycle $2,499 $3,248 SR 100, PE 2x50, 10X scRNA up to 1.2 billion
P3 50 cycle $1,884 $2,449 SR 50 up to 1.2 billion
         
P2 600 cycle $3,660 $4,758 PE 2x300 up to 300 million
P2 300 cycle $3,402 $4,423 SR 300, PE 2x150 up to 400 million
P2 200 cycle $2,689 $3,495 SR 200, PE 2x100 up to 400 million
P2 100 cycle $1,664 $2,163 SR 100, PE 2x50, 10X scRNA up to 400 million
         
P1 600 cycle $2,210 $2,873 PE 2x300 up to 100 million
P1 300 cycle $1,625 $2,113 SR 300, PE 2x150 up to 100 million
P1 100 cycle $1,310 $1,703 SR 100, PE 2x50, 10X scRNA up to 100 million

BACK TO TOP

__________________________________________________________


INCLUDED LIBRARY QC & QUANTIFICATION

All single tubes submitted for Illumina sequencing are quantified by qPCR, and fragment size distributions are measured using our AATI Fragment Analyzer.  There is no extra fee for these services (costs are included in the displayed sequencing rates).

However, if you are submitting mutliple tubes of individual libraries and wish for us to individually QC and multiplex them prior to sequencing, that is considered a separate Sample Prep request and costs an additional $12.50 per sample (on top of the standard sequencing price). Please contact jbishop2@uoregon.edu with questions!

BACK TO TOP

__________________________________________________________

SAMPLE SUBMISSION GUIDELINES

To submit a sample for sequencing, please register for an iLab account and then click "Request Services" from the top menu bar in iLab. It is important that your request has been submitted in iLab before you provide the physical samples to us!

Please submit 25 µL minimum volume per sample at 2-20 nM concentration in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable).

Please deliver samples to Jeff Bishop in 288 Klamath Hall if you are an on-campus user.  For off campus users, please mail samples frozen on ice in a well-protected vessel to the following address:

University of Oregon/GC3F
1318 Franklin Blvd
Room 273 Onyx Bridge
Eugene, OR 97403

NOTE: Please ensure that your package will arrive for delivery at UO only on Mon-Thurs. Due to campus restrictions during the COVID-19 pandemic, UO cannot accept deliveries on Fri-Sun.

BACK TO TOP

__________________________________________________________

GUIDELINES FOR CUSTOM SEQUENCING PRIMERS

If you'd like us to sequence a library that requires custom sequencing primers for any of the following reads:

Read 1, Read 2, Index 1 (i7), and/or Index 2 (i5)

We ask that you provide these custom sequencing primers along with your library.

Please submit 30 µL of each custom sequencing primer (per lane) at a concentration of 100 µM. Please be sure to make a note in the "comments" section of your sequencing submission about which custom primers you are including.

Thanks for your cooperation!

BACK TO TOP

__________________________________________________________

* Users from UO, OSU, and OHSU are eligible for Internal pricing. All other users are considered External.

NOTE: MiSeq and NextSeq may have multiple run types at the same price. This is because some reagent kits allow us the flexibility to sequence at multiple read lengths. However, since these kits cannot be subdivided, we are unfortunately not able offer a lower price for reads lengths that are shorter than the maximum allowed for the kit.

BACK TO TOP

 

​

 

We do our best to give an accurate estimate of turnaround time when service requests are submitted. These estimates are not guarantees and occasionally change due to unforeseen circumstances (instrument maintenance/repairs, staff sick leave, etc.). Please let us know if you have a hard deadline on project completion when you submit your service request and we will take measures to ensure that we either meet that deadline or inform you ASAP if circumstances beyond our control will cause us to miss it. Thanks!