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Old 05-12-2015, 06:50 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,091
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How about this?

Code:
$  awk '{if (/^>/) print ">Contig_"(++i)"_" substr($0,2); else print $0;}'  your_file > new_file
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