Ab5500Xl And Illumina Hiseq

Question

[dfernan]

Hi,

I am looking to buy a sequencing machine for our lab and was wondering if someone has had experience with both Illumina and AB biosystems. I was wondering about the differences between two sequencing machines by different companies, advantages and disadvantages.

I am looking into Illumina HiSeq 2500 and/or life technologies 5500 (AB5500xl).

More than a spreadsheet-type that I could find in the companies website I was wondering experience from researchers using both and what their thoughts are.

Thank you very much!

Answer 1

[matted]

This is only a partially informed answer from an informatics perspective, but it seems that Illumina is winning in mindshare and therefore in the number (and quality?) of downstream tools to do most analyses. I feel like more papers I read use Illumina sequencing, and I personally am happier to go back to raw data from Illumina (because of my familiarity) than dig through SOLiD data. Specifically, I believe the majority of sequencing done by big consortia like ENCODE and 1000 Genomes is on Illumina (though they do have some SOLiD data).

If you aren't familiar with the output of the two technologies, SOLiD outputs in Transforming And Manipulating Color Space Reads, which usually requires special handling or at least some careful thought. As evidence of its second-tier status (though that might be a controversial statement), the latest versions of the popular aligners bwa and bowtie 2 do not support color space reads.

[JC]

I agree with that, working in color-space limits the use of many software and could be painful. Besides, Life Tech is pushing more the Ion platform, so I believe the SOLiD will die soon.

[Ashutosh Pandey]

I agree with JC. Our university has two SOLiD 5500 XL machines but we will be replacing them with Ion platforms sometime end of this year. Ion platforms will have higher throughput and will provide nucleotide reads rather than color space coded reads.

Answer 2

[brentp]

Our lab had a SOLiD. It has given me nothing but trouble in terms of bioinformatics. Nearly every aligner (and downstream tool) is optimized for base-space calls and error profiles--with colorspace support added post-hoc without as much calibration. Many of the aligners do not report the base-qualities correctly for colorspace. None of the common downstream tools actually utilize the color information when making SNP calls.

While the SOLiD may deliver on its promise of more generated reads, in my experience, it has much lower mappability. That, combined with shorter read length and lower base-quality make it much less attractive for most applications. If you are only doing ChIP-seq and a bit of RNA-Seq, it may be OK (though I'd still favor Illumina or Proton), but not for anything with SNP-calling.

If you do use SOLiD, you will spend a lot more time (and therefore money) on bioinformatics.

All that said, if you really want to buy a SOLiD, I may know where you can get one at a huge discount. ;)

Answer 3

[JC]

Another option, I know at least 3 labs that are not buying new sequencers anymore because it's cheaper to send your samples (and get back your data) to sequencing centers. Check external costs.