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Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas #fasta #remove

Fastq 2 fasta. $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta #fastq #fasta #convert

Reformat you fasta sequence with size. $ seqkit seq -w 50 allGenomeContacted.fa > allGenomeContacted_final.fa #Reformat #Fasta #Size

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

Count the number of bases in fasta file. grep -v ">" file.fasta | wc | awk '{print $3-$1}' #Fasta #Count #Bases

Append the string to fasta header. $ sed 's/>.*/&_Bacteria/' foo.in > out.fasta #Sed #Fasta #String #Append

Filter #blank #lines from a #fasta file using sed. $ sed '/^$/d' finalSample.fa > finalSample_filtered.fa #Linux #Filter #FASTA #SED

fastq to fasta convertor $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta #Convert #Fasta #Fastq #fa #fq

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

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

Get the fasta sequence of the coordinates http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html #Fasta #Bed #Coordinates #Bedtools

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

Extract fasta sequence by Ids: perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #Perl #PerlOneliner #PerlTrick #Extract #Ids #Fasta