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Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

Add some text at the beginning of the file $ echo -e "chrII_reverse\n$(cat chrII_reverse.fa )" > chrII_reverse.fa #Add #FirstLine #Text

To add something to end of all header lines: $ sed 's/>.*/&WHATEVERYOUWANT/' file.fa > outfile.fa #Add #Fasta

Add ">" in front of ids. sed -e 's/^/prefix/' file #Sed #Add #>