Macrogen Vs Complete Genomics

Question

[Biomed]

We are pondering to outsource couple (around 20) whole human genome sequencing (mostly Mendelian disease/gene hunting in nuclear families) projects. Out two top candidates now are Macrogen (Illumina partner) and Complete Genomics.

My question is mainly to those who have worked with either of these companies and even better with both of them. What would your recommendations be? Are their data quality, services comparable? Also some other important things are turn around time and easy file formats, annotations so we can effectively pick up and continue the analysis down stream. Any comments regarding what type of strengths and weaknesses they have are much appreciated, I assume detection of snps would not change too much between two approaches but what about other things (i.e being able to detect larger indels, balanced translocations etc)? Do you have any specific recommendations that might help us in our decision?

Answer 1

[lh3]

I am not able to comment on macrogen. As to Complete Genomics (CG), you should ask yourself about how many analyses you want to do by yourself. CG has a very sophisticated pipeline. If you want to leave your project to them, CG will be a decent choice. However, if you want to get their data and analyze by yourself, you should watch out. While you have a variety of choices of software for analyzing Illumina data, the CG software package is pretty much the only one that is able to process the CG reads and alignments. When you have troubles with their results, you can hardly get help elsewhere except CG (their support seems good; I have sent them a couple of requests and all got replies in hours).

[Biomed]

Would this comment apply to the pipeline which would create a variant/genotype call output like mpileup output?

[Len Trigg]

The RTG Investigator package from www.realtimegenomics.com includes support for mapping (to SAM) and variant calling (to VCF) from Complete Genomics read data.

Answer 2

[Larry_Parnell]

Complete Genomics has made available data from 69 individuals. I picked up a copy on thumb drive at a recent conference but have yet to use those data. I know it is available from the web site. You could grab those data and take a look for yourself regarding data quality.

Check out the Assemblathon and ask those folks these same questions. While not directly related to your question, the Assemblathon was a test of different assembly algorithms but those involved surely would be able to comment on data quality.

[brentp]

I also wonder what Macrogen offers in terms of processed data. At least from CG's marketing, they offer pretty good variant calling and filtering.

[Biomed]

Assamblathon kindly declined to answer this question and refereed me to seqanswers eventhough I told them I had originally asked the question here and got refreed to their list:)

[Larry_Parnell]

OK, so they do not wish to take sides and are being diplomatic. That's fine. Did seqanswers give anything useful?