How Does NextSeq 500 Compare With MiSeq and HiSeq?

Illumina-NextSeq500-120Gb-400Million-2x150bp

Illumina-NextSeq500-120Gb-400Million-2x150bp

Illumina’s New year Bonanza came on time this year at JPM 2014. Announcing two new highthroughput sequencing systems NextSeq 500 and HiSeq X Ten, Illumina did not disappoint many. Illumina’s NextSeq 500 is the first desktop highthroughput sequencing system, that can perform Whole-Genome Sequencing, Exome Sequencing and RNA-Seq.

NextSeq 500 can run sequencing experiments in two modes; High Output and Medium Output.  For RNA-seq applications, NextSeq 500 can sequence

  • High Ouput mode: 10 mRNA sequencing samples in in 18 hours producing 40 Million paired end reads of length 2×75 bps
  • Medium Output mode: 3 mRNA samples in 15 hours producing the same number of reads with the same length.

For exome-seq applications, NextSeq 500  sequence 90% with 10X coverage with  similar number of samples and timing as above. And NextSeq 500 can sequence a human whole genome with 30X coverage using 2×150 bp reads in 29 hours.

Here we look at how does NextSeq 500 compare with Illumina’s existsing MiSeq and HiSeq solutions for sequencing using the Illumina data sheet.  

Whole-Genome Sequencing

How many large whole genome sequencing experiments (human genome at 30X coverage) in a single run?

  • MiSeq:  Not applicable
  • NextSeq 500: One
  • HiSeq 2500: 1 – 10

How many small whole genome sequencing experiments (30X or greater coverage of a 5 Mb microbial genome like E. Coli.) in a single run?

  • MiSeq:  1 – 96
  • NextSeq 500: 120-792
  • HiSeq 2500: 96-6660

Exome Sequencing

How many exome sequencing experiments (4 Gb per sample at 2×75 bp or 5 Gb at 2×100 read length) in a single run?

  • MiSeq:  1
  • NextSeq 500: 1 – 12
  • HiSeq 2500: 12 – 160

RNA Sequencing

How many RNA profiling experiments (10M reads per sample) in a single run?

  • MiSeq:  1 – 2
  • NextSeq 500: 12 – 36
  • HiSeq 2500: 24 – 396

How many Transcriptome Sequencing experiments (40M reads per sample) in a single run?

  • MiSeq:  Not applicable
  • NextSeq 500: 3 -10
  • HiSeq 2500: 8 – 96

How many small RNA sequencing experiments (5M reads per sample) in a single run?

  • MiSeq:  1 – 5
  • NextSeq 500: 25 – 80
  • HiSeq 2500: 60 – 792

Chip-Seq

How many Chip-Seq experiments (15M reads per sample for identification of transcription factor binding) in a single run?

  • MiSeq:  1
  • NextSeq 500: 8 – 24
  • HiSeq 2500: 20 – 264

Comments

  1. Yash Paul Khajuria says:

    I want to do transcriptome of sample having genome size of around 100Mb.
    Which allumina platform is best can I use Miseq Platform for that

  2. Michael M says:

    What is the difference here between “RNA profiling” and “Transcriptome Sequencing” as distinguished above? I understand the number of intended reads is different, but functionally what is the difference in the goal of the two lines of research?

    • Vincent says:

      RNA profiling is just to quantify gene expression. Transcriptome sequencing relates to more specific questions including splice variants, transposition, etc.

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