Tag Archives: MiSeq

Fast and Cost-Effective Bacterial Sequencing

The upgrade of the Illumina MiSeq promises 250 bp reads with a turnaround time in the paired-end module of ~ 35 hours. This upgrade is planned for Q3 so any day now it could happen.

Anyway I think that already the current version is an excellent alternative to other technologies when sequencing of bacterial genomes is of interest.

Since we only have the MiSeq since several weeks we want to add a bonus to bacterial sequencing on the MiSeq in our new special. The special delivers 2x 150 bp paired-end module reads for 2, 3, or 4 bacterial samples. The bioinformatic analysis like mapping against a reference genome and SNP/InDel detection can be ordered optinally. If you are interested in this special order before September 30th and profit from a 10% discount. Read more about our special here.

MiSeq – soon in its full bloom?

Rather than resting on the successes of the MiSeq launch, Illumina is continuously improving the performance of their small Benchtop Next Generation Sequencing System. Geoff Smith is talking about improvements in the read lenght of the MiSeq in the video attached.

This instrument is not only another next gen sequencing device but really has remarkable advantages over other instruments when sequencing for example bacterial genomes. This is why I am really delighted that we now can offer services using the MiSeq instrument. (More info on our MiSeq services can be found here)

16S Amplicon Experiments: Which Platform to Choose?

Since 2010 several studies have been published that analyze microbial community composition by amplicon sequencing on the Illumina Genome Analyzer (GA). However, direct adaption of these protocols for sequencing on the HiSeq 2000 – the currently predominant Illumina sequencer – is not possible as both systems use different basecalling pipelines. Therefore amplicon sequencing on Illumina HiSeq 2000 is still left to the very experienced users and only a few publications can be studied on this.

In the meanwhile Illumina has introduced the MiSeq as the optimal platform for this kind of projects. In this context they have published an application note presenting sequencing of the V4 region of 16S rRNA genes on the MiSeq system.

And I totally agree that the MiSeq is a very good tool for these studies. For me, the most important advantages of the MiSeq layout in comparison to the sequencing on Illumina HiSeq 2000 are as follows:

  • Shorter turnaround time: The sequencing run itself takes a bit more than one full day, while a HiSeq 2000 run takes up to 12 days.
  • More informational content: By overlapping two paired end reads of 150 bp, full-length reads of about 250 bp can be generated
  • Potential for even longer reads: Illumina has announced read length of 250 bp for the end of the year. Then reads of up to 450 bp should be possible.

Nevertheless Roche GS FLX+ sequencing is still able to generate much longer reads with an average of up to 500-600 bp. And the long read length will provide a deeper insight into the microbiome of interest or more precisely higher classification efficiency down to species level. However Roche sequencing goes along with higher costs per base, so it will always be a decision based on the individual experiment, whether read length or sequencing depth is the most important factor.

Product Launches 2011: The MiSeq at the Pole Position

Dear Blog Reader,

In our last NGS poll we asked you about your opinion, which of the product launches from 2011 would have the most impact on your research. We are delighted that more than 50 NGS blog readers gave us their vote.

More than half of you rated the launch of the benchtop sequencer MiSeq as the most important event in 2011. 15% voted for the Roche GS FLX+ technology and 15% voted for the increased data output with Illumina chemistry v3.0. PacBio RS sequencing and the new exomes on the market have the least importance for you (10% and 8%, respectively).

I also see the MiSeq benchtop sequencer as a door opener for many groups towards inhouse access to Illumina sequencing data. The investment for the technology is considerably lower than for the Illumina HiSeq 2000 or HiSeq 2500 and when having not too many projects the higher consumable cost per basepair may be acceptable. Furthermore the MiSeq stands out by its short run time of only several hours.

For a Service Provider using several Illumina HiSeq 2000 sequencer the MiSeq is very interesting, too. It can be used for resequencing and scaffolding of small genomes, for quality control of sequencing libraries and especially for developping new protocols and services.

Did you perform already first sequencing runs on the MiSeq and for what kind of projects do you think is the sequencer most suitable for? I am very much looking forward to hearing about your experiences.


The MiSeq Will Further Challenge the Roche 454 FLX+ Technology

Currently, Roche 454 has a unique selling proposition in providing the only sequencing technology on the market delivering long reads with high accuracy at the same time. Just last year Roche 454 launched the new GS FLX+ chemistry delivering reads with a modal read length of up to 700 bp. Long reads are crucial for de novo sequencing of genomes and transcriptomes and for sequencing of amplicons.

The current version of the Illumina MiSeq enables 2x 150 bp paired-end reads and 1.5 – 2 Gbp per run, which is slightly over the output of a typical GS FLX+ run. When working with short insert libraries of 200-250 bp, both paired-end reads will overlap and finally generate one longer read of up to 250 bp.

This read length is still not in a competitive range for Roche 454, but recently Illumina announced the launch of a MiSeq instrument upgrade by the middle of the year. According to Illumina ‘s vice president of marketing, the upgraded instrument will generate 2x 250 bp paired-end reads and up to 7 Gbp of data output. When sequencing short insert libraries with the 2x 250 bp paired-end module, reads with up to 450 bp can be generated. Thus, read length comes again closer to the read length of the Roche FLX+ technology (not to mention the 10x higher data output).

We have to wait and see whether the MiSeq upgrade keeps what Illumina promises, but for me personally it is quite clear, that with the announced specifications, the MiSeq will sooner or later replace Roche 454 sequencing for certain applications. In this light it is very interesting that Roche offered a friendly take over of Illumina this week.