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

Split the #multifasta to #singlefasta awk '$0 ~ "^>" { match($1, /^>([^:]+)/, id); filename=id[1]} {print >> filename".fa"}' input.fa

Multifasta 2 singlefasta cat toy.fasta| awk '{ if (substr($0, 1, 1)==">" {filename=(substr($0,2) ".fa")} print $0 > filename }' #Split #fasta #multifasta

Split a multi-FASTA file into individual FASTA files: awk '/^>/{s=++d".fa"} {print > s}' multi.fa #split #multifasta

perl -pe '/^>/ ? print "\n" : chomp' LR.fasta | tail -n +2 > out.fasta #singleLine #Multifasta #Multi2Single

#Split #multifasta $ cat hg18.fa | awk '{ if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")} print $0 > filename }'

Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa #Samtools #Fasta #Extract #Multifasta