NextGen Sequencing Information

There are several NextGen sequencing platforms on the market. Each platform operates using a unique combination of molecular chemistry and engineering/fluidics designs. As a result, read length, total base output, cost and data quality of each sequencing run varies with each platform.

The Center for Genome Innovation has the following sequencing platforms available for use:

  • Illumina: MiSeq (Available at both the Storrs and UConn Health locations)
  • Illumina: NextSeq 550 (Available at Storrs)
  • Illumina: NovaSeq 6000 (Available at Storrs)
  • Oxford NanoPore MinION and PromethION (Available at Storrs)
  • PacBio Revio and Sequel IIe (Available at Storrs)

Choosing the right platform

Choosing a platform for your experiment will depend on the type of sequencing (i.e. RNA-Seq, de novo genome sequencing, amplicon sequencing, etc.), desired coverage and budget you have. There are other important considerations to make in terms of read length and how long the experiment will take from start to finish. Given the complex nature of these experimental designs, the CGI’s staff will help you determine which platform is best suited to meet your goals. Upon request, Bo Reese will generate a platform-specific project budget and sequencing coverage analysis based on your experimental goals.

Here are links to the Specifications pages for each Illumina Platform:

MiSeq Specifications

NextSeq 550 Specifications

NovaSeq Specifications

When you purchase a sequencing kit, the number of cycles you get in the kit will vary.  To determine how much sequencing you can get from your Illumina kit, visit this page.

For more information about the PromethION system from Oxford Nanopore, visit their web page.

For more information about PacBio sequencing, visit their web page.

Protocols

The users of the CGI have adapted protocols and techniques for each of the NextGen platforms available for use in the Center in addition to the standard protocols provided by each company. Listed below are some of the most commonly requested library preparation/sequencing applications adapted by CGI users:

  • Whole genome shotgun sequencing
  • ddRAD-seq
  • ChIP-seq
  • RNA-seq (mRNA, total and micro RNA)
  • amplicon sequencing for any target
  • Methylation sequencing (enzymatic methyl-Seq)
  • Single Cell mRNA-Seq
  • Exome Sequencing