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Applications

The MiSeq supports a wide range of applications, including the following:

  • Targeted resequencing
  • TruSeq Custom Amplicon Sequencing
  • De novo sequencing (< 20Mb for ∼ 50x coverage, < 50Mb for ∼ 20x coverage)
  • Small RNA sequencing
  • Metagenomics
  • Library QC

The NextSeq500 supports a wide range of applications, including the following:

  • Whole genome sequencing
  • Exome sequencing
  • Transcriptome sequencing
  • Targeted resequencing
ApplicationMiSeqNextSeq500
DNA Sequencing
Whole Genome - Large (e.g. Human)1 1 1-10
Whole Genome - Small (e.g. E. coli)2 1-96 120-792
Targeted - Exome or large panels3 1 1-12
Targeted - Small gene panels4 3 15-48
RNA Sequencing
RNA Profilinga 1-2 12-36
Transcriptome Analysisb - 3-10
Small RNA Analysisc 1-5 25-80
Targeted RNAd 384 384
Regulation Applications
ChIP-Seqi 1 8-24
Methylation Analysisii - 1

DNA sequencing applications based on:

  1. 30x coverage of a human genome
  2. 30x or greater coverage of a 5 Mb microbial genome
  3. 4 Gb per sample at 2x75bp read length
  4. TruSight One Sequencing Panel

RNA sequencing applications based on:

  1. 10 million reads per sample
  2. 40 million reads per sample
  3. 5 million reads per sample
  4. based on TruSeq indexing and up to 65 targets for MiSeq, 1041 targets for NextSeq

Regulation sequencing applications based on:

  1. 15 million reads per sample for identification of transcription factor binding
  2. 30x coverage