Next-Generation Sequencing

The Genomics Core supports massively parallel high-throughput sequencing using next-generation sequencers. These sequencers can generate billions of bases of data per run to support a wide variety of applications. Researchers can choose either single or paired-end reads. Multiple samples can be indexed (barcoded) and combined in order to optimize the system's output.

The Genomics Core of the NARF operates HiSeq 4000, NextSeq 500, and MiSeq platforms from Illumina, a Sequel System from Pacific BioSciences, Ion Torrent and Proton platforms from Thermo Fisher Life Technology, and a 454 FLX+ system from Roche. Oxford NanoPore MinION technology is also available. A BioNano IRYS automated optical mapping platform for detection of large chromosomal rearrangements is also available in the Core. (Go to “Platforms” for more details)

A next-generation sequencing experiment can be broken down into 4 steps:

  • Experimental design (run type, desired output, read type)
  • Library construction
  • Sequencing runs
  • Data analyses

Sequencing costs vary depending on the application, size of genome and required depth and coverage. The table below summarizes the recommendations for standard experiments.

Please speak to us before planning a large experiment. We can guide you to make most efficient use of your budget.


CategoryApplicationOrganismRead Type1Coverage or Reads (millions)2
DNA Libraries
Genome SNVs Human 2x150 30x
Genome INDELs Human 2x150 60x
Genome Resequencing Bacterial 2x150 20x
Genome De novo sequencing Bacterial 2x300 50x
Exome SNVs Human 2x150 100x
Targeted ChIP-seq Human 2x150 15-50 M
Targeted FAIRE-seq Human 2x150 25-55 M
Methylation RRBS Human 2x150 10x
Methylation Bisulfite-Seq Human 2x150 30x
RNA Libraries
Transcriptome Expression profiling Human 1x75 10-25 M
Transcriptome Alternative splicing Human 1x75 50-100 M
Transcriptome De novo assembly Human 1x75 100 M
Transcriptome Expression profiling Bacterial 1x75 10 M
Small RNA Expression profiling Human 1x75 1-2 M
Small RNA Discovery Human 1x75 5-8 M

1 Optimal sequence read length depends on the strategy and the objective. Please discuss this with us before deciding.

2 Generally, more coverage is better, but sometimes it is wasted sequencing power and money. Coverage depends on the anticipated outcome and purpose, and of course budget. Again, please see us for optimal use of your research dollars.