I don't think there is a significant difference in the lab work. These are the main differences I have read about;
(1) Although 23andMe has the largest database for relative matching, a large portion of the test subjects are interested only in the health aspects. Thus, the % of responses to sharing request is low. The number of responses at FTDNA are roughly the same, even though their database is considerably smaller.
(2) Ancestry's database is almost as large as 23andMe's and most are interested in genealogy. However, there are complaints about anonymous subjects mooching off of those who post trees publicly.
(3) Ancestry does not have a chromosome browser.
(4) FTDNA's genealogical tools are much better than 23andMe's, which are really clunky.
You can upload your 23andMe or Ancestry results to FTDNA for $69, occasionally on sale at $49.
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