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Delete all the headers from multifasta file $ awk 'BEGIN {print ">"ARGV[1]};!/^>/{print}' test.fa #fasta #delete #header #multifasta

Perl onliner to add string to each of the fasta header. $ perl -p -e 's/^(>.*)$/$1-origin/g' in.fasta > out.fasta #String #Header #Fasta

#Rename the #fasta #header and #keep first $ perl -ne 'if (/^(>\S+)/){print "$1\n";}else{print $_;}' realTestDATA.fa > realTestDATA_headerCorrected.fa #Perl

One liner to remove the description information from a fasta file and just keep the identifier $ perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #clean #header #fasta

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

Rename the fasta header perl -ane 'if(/\>/){$a++;print ">LR$a\n"}else{print;}' allPacBio_clean.fa > allPacBio_clean_shortName.fa #fasta #header #rename

Remove "|" from fasta header. $ sed 's,|,_,g' -i file.fa #fasta #header #sed

Remove unwanted character from fasta file. sed -e '/^[^>]/s/[^ATGCatgc]/N/g' file.fa #fasta #file #header #charater

Remove the unnecessary #fasta #header. $ sed 's/\s.*$//' Adineta_vaga_v2.0.scaffolds.fa > new_file.fasta

To clean up a fasta file so only first column of the header is outputted:$ awk '{print $1}' file.fa > output.fa #Sed #Clean #Header #Fasta