Major Applications


Illumina NextSeq 550: allows for analysis of mid-sized genome re-sequencing or transcriptome sequencing projects​

NextSeq 550  (run duration: 8-30 hours)

The NextSeq uses a 4 lane flow cell that is clustered with a single library pool, the flow cell has two run types High Output (NX-HO) and Mid Output (NX-MO).  The High Output flow cell can produce 360-400 million reads per run with read lengths up to 150 bp, single or paired end, while the Mid Output flow cell can produce 117-130 million reads per run with read lengths up to 150 bp, single or paired end.  

Illumina MiSeq: allows for more targeted sequencing of smaller genomes and amplicons

MiSeq  (run duration: 8-50 hours)

Uses a single lane flow cell and can produce 15-25 million reads per run with read lengths up to 300 bp, single or paired end. This sequencing system is good for metagenomic studies. MiSeq runs can also serve as a way of quality checking library preparations prior to running on the NextSeq or HiSeq.

MiSeq has a smaller output flow cell producing 1 million (MiSeq Nano) or 4 million (MiSeq Micro) reads, which can be used for sequencing library QC and small amplicon sequencing projects.


Applications and Recommended Run Types

1.  Whole Genome Sequencing and Re-Sequencing (DNA-seq):

  •      Genome re-sequencing: mutant identification, evolutionary comparisons, disease tissue sequencing: 
    •      Single read 100 (SR100) or paired end 100 (PE 100)
  •      De novo genome assembly for new unsequenced species:
    •      ​PE100 or PE150

2.  Expression/Transcriptome Analysis (RNA-seq):

  •      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

3.  Epigenomics and Gene Regulation:

  •      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

4.  Metagenomics, Amplicon, or Targeted Gene Sequencing:

  •       MiSeq
    • V2 and V3 reagents produce 15-20 million reads - good for Metagenomic or Targeted Gene sequencing projects
    • Micro reagents produce 4 million reads ​- Nano reagents produce 1 million reads
      • good for QC of custom library preps or small scale amplicon sequencing projects

Note: Users can download the Illumina Sequencing Coverage Calculator to estimate the number of lanes of sequencing required for your experiment. 

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