SGT Resources

Here are our favorite resources about next generation sequencing (NGS) as well as information about the sequencing platforms we house. If you’re new to NGS, please check out this beginners guide.

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Nucleic Acid Extraction Resources

We offer various extraction services and perform quality control on all nucleic acids. We recommend reading our extraction resources below if you are performing extractions or need refreshers on quality control checks.

We measure DNA concentrations with Qubit and band sizes for possibly degraded DNA with the Agilent Bioanalyzer. Here is quick refresher on genomic DNA quantity and quality.
*Please note: NanoDrop Spectrophotometers can overestimate concentrations. Take this into consideration if submitting samples that have been quantified this way.

For Illumina sequencing, we recommend the following kits for genomic DNA extractions:

For long read sequencing, we recommend the following kits for high molecular weight genomic DNA extractions:

We measure RNA concentrations with Qubit and band sizes with the Agilent Bioanalyzer. Here is a quick refresher on RNA quality. We strongly recommend DNase treatment on RNA samples.
*Please note: NanoDrop Spectrophotometers can overestimate concentrations. Take this into consideration if submitting samples that have been quantified this way.

We recommend the following kits for RNA extractions:

Short Read Sequencing

Illumina’s Next Generation Sequencing technology uses sequencing by synthesis (SBS) chemistry and allows for both single-read and paired-end sequencing options up to 300 bp in length.

We offer short read sequencing services on our Illumina NovaSeq X Plus, MiSeq, and NextSeq 1000 sequencers. As all Illumina sequencers use similar chemistry, same library preparations can be used across these instruments, allowing us to tailor to researchers’ sequencing needs according to read length, throughput, and turnaround time. Illumina provides sequencing coverage recommendations to help determine how many reads are needed for an experiment.

Multiple samples can be indexed by a unique nucleotide sequence and pooled into an individual run to save costs. Samples may be indexed using Illumina’s TruSeq indices, Nextera indices, or custom indexing adaptors. The SGT can demultiplex the reads and provide fastq files for each individual sample if Illumina indices are used.
*Please note: If submitting customer prepared libraries, each library must contain a unique index barcode to allow for pooling and accurate demultiplexing. Indexes cannot be reused for libraries in the same pool.

The NovaSeq X Plus is a the latest robust and flexible, production-scale sequencer from Illumina that utilizes patterned flow cells and novel 2-color channel XLEAP chemistry. XLEAP chemistry reduces reagent costs and decreases data processing times while still producing the same high-quality data. The NovaSeq X also allows the flexibility to sequence by flow cell or lane.

SEQUENCING OUTPUT PER FLOW CELL

Product # of Cycles Total Reads per Flow Cell Total Reads per Lane Output (Gb) Duke Price Non-Profit External Price
1.5B flow cell

100 Cycles
(50x50)

1.5 B n/a 150 $2,589 $2,999
1.5B flow cell 200 Cycles
(100x100)
1.5B n/a 300 $3,139 $3,576
1.5B flow cell 300 Cycles
(150x150)
1.5 B n/a 450 $3,359 $3,807
1.5 B lane Any Config n/a 700 M variable $1,929 $2,306
10B flow cell 100 Cycles
(50x50)
10 B n/a 1,000 $10,798 $13,012
10B flow cell 200 Cycles
(100x100)
10 B n/a 2,000 $12,888 $15,206
10B flow cell 300 Cycles
(150x150)
10 B n/a 3,000 $13,548 $15,899
10B lane Any Config n/a 1 B variabl $1,818 $2,188
25B flow cell 300 Cycles
(150x150)
25 B n/a 8,000 $22,832 $26,904
25B lane Any Config n/a 3 B variable $2,872 $3,504

The MiSeq is a benchtop sequencer from Illumina that allows for more focused applications, such as targeted gene sequencing, metagenomics, small genome sequence, targeted gene expression, and amplicon sequencing. The ability to run long paired-end reads (2 x 250bp or 2 x 300bp) makes this instrument ideal for amplicon sequencing. The MiSeq is capable of generating ~12 million reads passing filter for v2 kits (~24 million for paired-end sequencing) and ~22 million reads passing filter for v3 kits (~44 million for paired-end sequencing).

Flow Cell # of Cycles Total Reads per Flow Cell Total Reads per Lane Output (Gb) Duke Price Non-Profit External Price
MiSeq NANO V2

300 Cycles
(150x150)

1 M n/a 0.3 $808 $1,088
MiSeq NANO V2 500 Cycles
(250x250)
1 M n/a 0.5 $886 $1,169
MiSeq MICRO V2 300 Cycles
(150x150)
4 M n/a 1.2 $1,004 $1,293
MiSeq V2 50 Cycles
(50 SR)
12 M n/a 0.75 $1,500 $1,814
MiSeq V2 300 Cycles
(150x150)
12 M n/a 4.5 $1,802 $2,131
MiSeq V2 500 Cycles
(250x250)
12 M n/a 6.0 $1,973 $2,311
MiSeq V3 150 Cycles
(75x75)
22 M n/a 3.3 $1,619 $1,939
MiSeq V3 600 Cycles
(300x300)
22 M n/a 13.2 $2,439 $$2,800

The NextSeq 1000 is a new benchtop sequencer from Illumina that utilizes a patterned flow cell, 2-color channel chemistry, and an integrated sequencing cartridge. The patterned flow cell features a novel, high resolution optical system and higher cluster densities to allow for increased data output with greater resolution. Two flow cell types are offered to help cater to coverage needs: P1 and P2.

Flow Cell # of Cycles Total Reads per Flow Cell Total Reads per Lane Output (Gb) Duke Price Non-Profit External Price
NextSeq 1000 XLEAP P1 100 Cycles
(50x50)
100 M n/a 10 $1,227 $1,533
NextSeq 1000 XLEAP P1 300 Cycles
(150x150)
100 M n/a 30 $1,535 $1,862
NextSeq 1000 XLEAP P1 600 Cycles
(300x300)
100 M n/a 60 $1,956 $2,457
NextSeq 1000 XLEAP P2 100 Cycles
(50x50)
400 M n/a 40 $1,637 $1,964
NextSeq 1000 XLEAP P2 200 Cycles
(100x100)
400 M n/a 80 $@,694 $3,073
NextSeq 1000 XLEAP P2 300 Cycles
(150x150)
400 M n/a 120 $3,430 $3,846
NextSeq 1000 XLEAP P2 600 Cycles 400 M n/a 240 $3,695 $4,124
Flow Cell # of Cycles Total Reads per Flow Cell Total Reads per Lane Total GBP Duke Price Outside of Duke Price
MiSeq NANO V2 300 Cycles (150x150) 1 M n/a 0.3 $808 $1088
MiSeq NANO V2 500 Cycles (250x250) 1 M n/a 0.5 $886 $1,169
MiSeq MICRO V2 300 Cycles (150x150) 4 M n/a 1.2 $1004 $1,293
MiSeq V2 50 Cycles
(50 SR)
12 M n/a .75 - .85 $1,500 $1,814
MiSeq V2 300 Cycles (150x150) 12 M n/a 4.5 $1,802 $2,131
MiSeq V2 500 Cycles (250x250) 12 M n/a 6.0 $1,973 $2,311
MiSeq V3 150 Cycles (75x75) 22 M n/a 3.3 $1,619 $1,939
MiSeq V3 600 Cycles (300x300) 22 M n/a 13.2 - 15 $2,439 $2,800
NextSeq 1000 P1 100 Cycles (50x50) 100 M n/a 10 $1,227 $1,533
NextSeq 1000 P1 300 Cycles (150x150) 100 M n/a 30 $1,535 $1,862
NextSeq 1000 P1 600 Cycles (300x300) 100 Million n/a 60 $1,956 $2,457
NextSeq 1000 P2 100 Cycles (50x50) 400 M n/a 40 $1,637 $1,964
NextSeq 1000 P2 200 Cycles (100x100) 400 M n/a 80 $2,694 $3,073
NextSeq 1000 P2 300 Cycles (150x150) 400 M n/a 120 $3,430 $3,846
NextSeq 1000 P2 600 Cycles (300x300) 400 M n/a 240 $3,695 $4,124
NovaSeq X 1.5B 100 Cycles (50x50) 1.5 B n/a 150 $2,589 $2,999
NovaSeq X 1.5B 200 Cycles (100x100) 1.5 B n/a 300 $3,139 $3,576
NovaSeq X 1.5B 300 Cycles (150x150) 1.5 B n/a 450 $3,359 $3,807
NovaSeq X 1.5B Any Config n/a 750 M variable $1,929 $2,306
NovaSeq X 10B 100 Cycles (50x50) 10 B n/a 1,000 $10,798 $13,012
NovaSeq X 10B 200 Cycles (100x100) 10 B n/a 2,000 $12,888 $15,206
NovaSeq X 10B 300 Cycles (150x150) 10 B n/a 3,000 $13,548 $15,899
NovaSeq X 10B Any Config n/a 1 B variable $1,818 $2,188
NovaSeq X 25B 300 Cycles (150x150) 25 B n/a 8,000 $22,832 $26,904
NovaSeq X 25B Any Config n/a 3 Billion variable $2,872 $3,504

Long Read Sequencing

Long read sequencing, also known as third generation sequencing, involves reading sequences that are thousands of bases long. The longer read length generates a reasonable amount of overlap between sequences for better sequence assembly. We offer long read sequencing on the PacBio Revio sequencer.

Single Cell

Single-cell sequencing can provide genomic, transcriptome, or multi-omics information from a single-cell. We offer single-cell sequencing on the Mission Bio Tapestri Platform.