High Throughput Sequencing

At the GRCF High Throughput Sequencing Center, our goal is to provide the research community at Johns Hopkins University with access to ‘next generation’ sequencing platforms. We currently feature three HiSeq 2500 instruments two MiSeq instruments, and a NovaSeq6000.  We do our best to sequence samples in a timely manner, but our primary focus is on generating high quality data.

We offer simple, per lane and per flow cell pricing, along with end to end service for whole exome/custom targeted projects, RNASeq, and whole genome.

NovaSeq Pricing

NovaSeq Order
NovaSeq runs are fixed, but include additional cycles for dual indexed libraries.

SP: ~1.6 billion paired reads, ~800 million single reads	S1: ~3.2 billion paired reads, ~1.6 billion single reads	S2: ~8.2 billion paired reads, ~4.1 billion single reads	S4: ~20 billion paired reads, ~10 billion single reads
100 cycle: $3600	100 cycle: $6700	100 cycle: $11,300
300 cycle: $5200	200 cycle: $8700	200 cycle: $15,000	200 cycle: $27,000
500 cycle: $6800	300 cycle: $9900	300 cycle: $17,100	300 cycle: $33,000

HiSeq2500 Flowcell Pricing (Rapid Mode)

Per Flowcell Order

Single Read Flowcell: ~300 million reads	Paired End Flowcell: ~600 million reads
50 bp: $2000 per flowcell	50 bp (x2): $3400 per flowcell
75 bp: $2400 per flowcell	75 bp (x2): $4000 per flowcell
100 bp: $2800 per flowcell	100 bp (x2): $4400 per flowcell
150 bp: $3600 per flowcell	150 bp (x2): $5400 per flowcell

HiSeq2500 Lane Pricing (Rapid Mode)

Per Lane Order

Single Reads Per Lane: ~150 million reads	Paired End Reads Per Lane: ~300 million reads
50 bp: $1,200 per lane	50 bp (x2): $1,900 per lane
100 bp: $1,600 per lane	100 bp (x2): $2,400 per lane
150 bp: $2,000 per lane	150 bp (x2): $2,900 per lane

Non-standard read lengths are also available for Per Flowcell orders. Please inquire about pricing.

High Output Runs are available, but you should consider the NovaSeq for high throughput applications, as the cost per base will be cheaper.

Sample Requirements

Completed Libraries: Please submit 10μl of your sample at 2nM.  Samples must be pooled.  We will do a QC check via Bioanalyzer to increase the likelihood of quality data, but you should quantitate your sample as accurately as possible.  Nanodrop is not reliable.  qPCR is by far the most accurate, but intercalating dye methods can be used.

Library Prep:  $250/sample.  Please provide us with >500ng of high molecular weight DNA/RNA.  Please contact us to discuss sample submission.

Data Yield

Our facility features the HiSeq 2500 platform. We almost exclusively run our instruments in Rapid Run Mode, due to the fast run times and low error rates. Yield is dependent upon several factors:

• Read Length: the longer the read, the more data.
• Read Type: paired end reads yield twice the data as single read.
• Optimal Cluster density: it is imperative to accurately quantitate your library to ensure high data yield. We do our best to QC libraries before sequencing, but we cannot pool samples for you.
• High Quality Library: libraries that contain a high level of adapter dimers will yield significantly less data, particularly on the NovaSeq6000. Similarly, over amplified libraries can negatively impact yield.
• Uniform Base composition: while less of an issue than in the past, libraries that have uneven base composition tend to pose problems with the HiSeq analysis software. These issues can be mitigated using several strategies, but the net effect will be lower data yield per lane than a balanced library.

Please see Illumina’s HiSeq 2500 and NovaSeq6000 Specification page for current data yields. While we regularly achieve greater than ‘spec’ yields from the HiSeq2500 and NovaSeq6000, typicially matching yields, it is best to be conservative when planning your experiments.

Data Delivery

Per lane/flowcell sequencing:  Data will be returned in Sanger FASTQ format via our high speed aspera server

End to end services:  alignment files, variant calls, and any intermediate files you wish via aspera server

 

Place Order