Next-Generation Sequencing

Next-Generation Sequencing

Library preparation, sequencing, bioinformatics.

RNAseq, ChIPseq, ATACseq, CRISPR screening, or something new!

Next-Generation Sequencing Platforms

Illumina Sequencing by Synthesis

Need a refresher? This 5 min. video from Illumina might help.

Sequencing reagents are priced by the number of “cycles”. Sequencing by synthesis means that 1 chemistry cycle = 1bp.  Cycles are typically divided symmetrically. For example, a 150cycle reagent kit is typically used to perform paired-end 75bp sequencing. However, cycles can be allocated asymmetrically (upon request) for customized read lengths such as 37bp X 51bp.


The Illumina MiSeq is a single-lane “low-throughput” sequencer.
Version 2 chemistry (v2): 12-15M clusters (reads or read pairs)
Version 3 chemistry (v3): 20-25M clusters (reads or read pairs)


Reagent Kit Clusters DFCI External
50cycle (v2) 12-15M $850 $950
150cycle(v3) 20M $1,200 $1,300
300cycle(v2) 12-15M $1,200 $1,300
500cycle(v2) 12-15M $1,600 $1,700
600cycle(v3) 20M $2,000 $2,200


The Illumina Minieq is a single-lane “low-throughput” sequencer that generates 35M clusters (reads or read pairs) per run.


Reagent Kit Clusters DFCI/BWH External
75cycle 30-35M $1200 $1400
150cycle 30-35M $1,400 $1,600
300cycle(v2) 30-35M $1,750 $2,500


The Illumina NextSeq500 is a fast high throughput sequencer that is capable of generating data from >400M clusters in 12-30hrs.

Mid Output (MO) = 130M clusters (reads or read pairs)
High Output (HO) = 400M clusters (reads or read pairs)


Reagent Kit Clusters DFCI External
75cycle (HO) 400M $2,200 $2,860
150cycle (MO) 130M  $2,200  $2,860
150cycle (HO) 400M $4,000 $5,200
300cycle (MO) 130M  $2,500  $3,250
300cycle (HO) 400M $6,500 $7,250


With 800M, 1.6B, 3.3B, or 10B clusters (reads or read pairs) per flow cell, this is Illumina’s highest throughput DNA sequencer to date.
Highly flexible flowcell and reagent configurations facilitate cost-effective sequencing for large scale genomics research including single-cell applications, whole genome, whole transcriptome, and whole genome methylation profiling.

For more information click here