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But Kerr was sacked when the Republic failed to qualify for next year's World Cup finals in Germany.
"It was an honour when Brian asked me to be his assistant but I was always under the impression that any agreement only ran in line with his own position," Hughton told the Mail on Sunday.
"I really enjoyed working with different players at international level and I will miss it. Personally, I think it was the wrong decision to get rid of Brian. If you look at his record, it was extremely good against some difficult opposition."