Major Applications and Ideal Run Types

Illumina MiSeq, NextSeq550, and NextSeq2000 Specifications
	Illumina MiSeq	Illumina NextSeq550	Illumina NextSeq2000
Run Duration	4-55 hours	12-30 hours	11-48 hours
Flow Cell Type	Non-Patterned Single lane	Non-Patterned High-Output or Mid-Output	Patterned P1, P2, or P3
Number of Reads	Nano: 1 million Micro: 4 million V2: 13-15 million V3: 20-25 million	High-Output: 360-400 million Mid-Output: 117-130 million	P1: 100 million P2: 400 million P3: 1100 million
Read Length	Up to 300 bp (Single-Read or Paired-End)	Up to 150 bp (Single-Read or Paired-End)	Up to 300 bp (P1 & P2) Up to 150 bp (P3) (Single-Read or Paired-End)
Ideal Project Type	Metagenomics Amplicon Small-Genome	Transcriptome Single Cell mRNA miRNA/small RNA	Exome WGS

Whole Genome Sequencing and Re-Sequencing (DNA-seq)

Single Read (SR) / Paired End (PE)

Genome re-sequencing: mutant identification, evolutionary comparisons, disease tissue sequencing:

SR100 or PE 100

De novo genome assembly for new unsequenced species:

PE100 or PE150

Single Read (SR) / Paired End (PE)

De novo transcriptome analysis in an unsequenced or unannotated genome:

PE100 or PE150

RNA-seq to study comparative transcriptomics in model genomes (e.g. sequenced and annotated genomes):

SR50 or SR100

Small RNA transcriptomics:

SR50

Single Read (SR) / Paired End (PE)

Chromatin immunoprecipitation sequencing (ChIP-seq) to identify transcription factor interaction sites:

SR50 or SR100

Methylated DNA sequencing to identify methylated regions of the genome:

SR100, PE100, or PE150

depending on the extent of annotation of the reference genome

Single Read (SR) / Paired End (PE)

Illumina MiSeq System

Nano reagents produce ~1 million reads

Micro reagents produce ~4 million reads

Good for QC of custom library preps or small scale amplicon sequencing projects

V2 and V3 reagents produce ~15-25 million reads

Good for Metagenomic or Targeted Gene sequencing projects