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?