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, High Output Flowcell
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
NextSeq500, Mid Output Flowcell      
Single-end 150 bp   130-200 19-30
Paired-end 2 x 75 bp   260-400 19-30
Paired-end 2 x 150 bp   130-200 38-60

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

*NEW* We have a site for Cornell users wishing to share Metagenomic MiSeq runs. Information can be found at this link --CURRENTLY TESTING

 

Link to Sample Submission Instructions      Fragment Analyzer QC interpretation

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 (SE 1 x 50 bp) ~1 day 12-15 0.6-0.75
300 bp kit (PE 2 x 150 bp) ~1.5 days 24-30 3.6-4.5
500 bp kit (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 (PE 2 x 300 bp) ~3 days 44-50 13-15
MiSeq Nano kits      
300 bp kit (PE 2 x 150 bp)   2 0.3
500 bp kit (PE 2 x 250 bp)   2 0.5
MiSeq Micro kit      
300 bp kit (PE 2 x 150 bp)   8 1.2

 

*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      Fragment Analyzer QC interpretation

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.