Ion Torrent vs MiSeq & GS FLX+

[Kanak Vaidya]

Which would be the better option for whole transcriptome analysis of bacterial genomes: Ion Torrent 316 chip, MiSeq or GS FLX+ ?

[westerman]

The FLX because it has longer reads. Potential problem is homopolymers especially if your bacteria are GC-rich or GC-poor.

[krobison]

Is this de novo to determine the transcriptome or expression profiling?

FLX will always be at a disadvantage on profiling due to much lower read counts.

FLX will be easier to assemble into a transcriptome due to the long reads, but my impression is that the 2x150 reads on the Illumina platform are rapidly eroding that. It's not my area, but I'd probably go with MiSeq for this application.

[westerman]

Is this de novo to determine the transcriptome or expression profiling?

FLX will always be at a disadvantage on profiling due to much lower read counts.

FLX will be easier to assemble into a transcriptome due to the long reads, but my impression is that the 2x150 reads on the Illumina platform are rapidly eroding that. It's not my area, but I'd probably go with MiSeq for this application.

Hi Keith. Always enjoying reading your Omics blog.

I probably should have put a smiley face disclaimer in front and in back of my reply to the original poster. Kanak Vaidya simply did not give enough information to make an informed choice in the matter. This was sort of like choosing between chocolate, strawberry and vanilla single or triple-dip in a regular cone or a premium sugar cone without knowing anything about the person's tastes and finances.

I did have a longer response for my original post but the system ate it (due to my stupidity in pressing the wrong button.) That longer response started off with "If time and money considerations are of no concern ..." in which case the FLX+ with 700 base reads is a winner especially for de-novo work (which is what I mainly do) especially since the Newbler software provides for a very nice transcriptome analysis. On the other hand the MiSeq with simple sample prep, quick turnaround, and cheaper per-base cost is good for known transcripts (which is my impression what you mainly do) since those 100-150 bp reads map very nicely. Yet on the third hand where are the FLX+ and MiSeq machines? Rare at the moment. So maybe the Ion Torrent would be a better choice. If we are talking 'future' then the 318 and further chips will be tasty.

In the end they all have advantages, or more importantly disadvantages, and until Kanak Vaidya can give us more details then we are just guessing at which system would be best for him.

Kanak, can you chime in with more details on what you want to do and your financial and bioinformatics support? Also read Keith's blog (http://omicsomics.blogspot.com/) -- lots of good information in there.

[Michael.James.Clark]

MiSeq is on the order of five bacterial genomes per 8 hour run if I'm correct? Seems like it'd be a great choice, especially since it's an all-in-one package now.

IT316 might be good too, though I'm still questioning the quality of the bases on the end, the robustness against homopolymers and the overall analysis at this point. MiSeq seems like a safer bet at the moment to me.

[epistatic]

I'm liking 6M PE-150 reads on a MiSeq more than 100K 450 bp reads on the 454 FLX.

[SeqAA]

I'm liking 6M PE-150 reads on a MiSeq more than 100K 450 bp reads on the 454 FLX.

I'd rather have long reads if this was bacterial de novo though.
It's all a give and take I guess.

[lek2k]

For Ion Torrent vs MiSeq. Read this in depth independent analysis

http://www.edgebio.com/blog/?p=241

For Ion Torrent vs 454

http://flxlexblog.wordpress.com/2011/08/10/iontorrent-longer-reads-longer-homopolymers/

[rtp115]

Anyone in this forum get his/her hands on one of the early access MiSeq? Would like to hear about your experience so far.