Next generation sequencing

The Illumina NextSeq500 instrument is capable of generating approximately 400 million reads per run passing filter, or up to 800 million reads per run passing filter for paired-end sequencing. Current read lengths available are single-end 75 bp, single-end 150 bp, paired-end 2 x 75 bp, and paired-end 2 x 150 bp. This instrument runs one sample (or pool of samples) on a run, and custom read lengths may be available. Please see the Illumina website for detailed specifications for this instrument.

NextSeq500 Run Time Reads Passing Filter (M)/lane Pass Filter Output (Gbp)/lane
Single-end 75 bp 12 hours 333-400 25-30
Single-end 150 bp* 18 hours 333-400 50-60
Paired-end 2 x 75 bp* 18 hours 666-800 50-60
Paired-end 2 x 150 bp 30 hours 666-800 100-120

* special order

*NEW* We have a site for Cornell users wishing to share NextSeq500 or MiSeq runs. Information can be found at this link

Link to Sample Submission Instructions

Link to Genomics Price List

 

The Illumina HiSeq2500 instruments, operating in "High Output Mode" and running Illumina's v4 chemistry are capable of generating up to 250 million reads per lane passing filter, or up to 500 million reads passing filter for paired-end sequencing. Current read lengths available are single-end 50 bp, single-end 100 bp, and paired-end 2 x 125 bp.

In High Output Mode and version 4 chemistry, 8 lanes of samples are required to do a run of any run type, so turnaround time may be affected. If rapid turnaround times are needed, consider performing a NextSeq500 run or a "Rapid Run," below.

HiSeq2500 High Output Mode, v4 chemistry
Run Time Reads Passing Filter (M)/lane Pass Filter Output (Gbp)/lane
Single-end 50 bp ~2 days 222-250 11-12.5
Single-end 100 bp ~3 days 222-250 22-25
Paired-end 2 x 125 bp* ~6 days 444-500 55-62.5

* though possible, this run length is not common for us, so unless you are running a full flowcell of 8 lanes, the turnaround time will be slow.

 

Link to Sample Submission Instructions

Link to Genomics Price List

 

The Illumina HiSeq2500 instruments, operating in "Rapid Run Mode" are capable of generating approximately 135 million reads passing filter per lane, or up to 270 million reads passing filter per lane for paired-end sequencing. This is a two-lane flowcell.

HiSeq Rapid Run Mode Run Time Reads Passing Filter (M)/run Pass Filter Output (Gbp)/run

Single-end 50 bp -- One sample (or pool) in BOTH lanes

~1 day  235-270  12-14

Single-end 100 bp -- One sample (or pool) in BOTH lanes

~1.5 days  235-270  24-27

Paired-end 2 x 100 bp -- One sample (or pool) in BOTH lanes

~2 days  470-540  48-54

Paired-end 2 x 150 bp -- One sample (or pool) in BOTH lanes

~2.5 days  470-540  70-80

Paired-end 2 x 250 bp -- One sample (or pool) in BOTH lanes

~3 days  470-540 117-135

Single-end 50 bp -- One sample (or pool), one lane

~1 day  115-135  6-7

Single-end 100 bp -- One sample (or pool), one lane

~1.5 day 115-135 12-14

Paired-end 2 x 100 bp -- One sample (or pool), one lane

~ 2 days 235-270 24-27

Paired-end 2 x 150 bp -- One sample (or pool), one lane

~ 2.5 days 235-270  35-40

Paired-end 2 x 250 bp -- One sample (or pool), one lane

~3 days 235-270 59-67

Link to Sample Submission Instructions

Link to Genomics Price List

 

The Illumina MiSeq instruments are capable of generating approximately 20 million (v2 kits) - 28 million (v3 kits) raw reads per run, or up to 40 million - 56 million raw reads for paired-end sequencing. Typically 80-90% of these reads pass filtering. Currently, v2 kits are available for 50 bp, 300 bp, and 500 bp runs and v3 kits are available for 150 bp and 600 bp runs. The runs may be configured with some flexibility, e.g. a 50 bp kit can be used for a paired-end 2 x 25 bp run. This platform is ideal for sequencing small genomes or amplicon sequencing projects. The ability to run long paired-end reads (either 2 x 150 bp, 2 x 250 bp, or 2 x 300 bp) makes this instrument ideal for de novo assembly of small genomes.

MiSeq v2 kits
Run Time Reads Passing Filter (M)/run Pass Filter Output (Gbp)/run
50 bp kit (e.g. SE 1 x 50 bp) ~1 day 12-15 0.6-0.75
300 bp kit (e.g. PE 2 x 150 bp) ~1.5 days 24-30 3.6-4.5
500 bp kit (e.g. PE 2 x 250 bp) ~2 days 24-30 7.2-9
MiSeq v3 kits      
150 bp kit, SE 1 x 150 bp ~1.5 days 22-25 3.3-3.75
150 bp kit, PE 2 x 75 bp ~1.5 days 44-50 3.3-3.75
600 bp kit (e.g. PE 2 x 300 bp) ~3 days 44-50 13-15

 

*NEW* We have a site for Cornell users wishing to share NextSeq500 or MiSeq runs. Information can be found at this link

Link to Sample Submission Instructions

Link to Genomics Price List

 

Pooling Samples/Barcoding/Indexing options: For Illumina sequencing, multiple samples can be pooled into an individual lane. Samples may be indexed by using Illumina's TruSeq indices, Illumina's Nextera indices, or custom indexing adaptors. If the indexing is using the Illumina strategy (the indexes are embedded in the adaptors and read as a separate indexing read or reads), the Genomics Facility will be able to separate the reads and provide fastq files for each individual sample. If custom indices are used, the sequences will have to be provided to the lab prior to the run.

 

Data Archiving/Retrieval: Illumina data are available for download for 30 days. After 30 days, an additional charge may be applied for recovering the run from archive.

 

 

Link to Sample Submission Instructions

Link to Genomics Price List