Fast rename fasta header

# Rename all the header in a FASTA file with a sequential posix (e.g., Seq_1, Seq_2, ...)
awk '/^>/{print ">Seq_" ++i; next}{print}' input.fasta > output.fasta
# Or with in-place edit with moreutils sponge
awk '/^>/{print ">Seq_" ++i; next}{print}' input.fasta | sponge input.fasta

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