BOL

Count number of fasta sequence $ awk '/^>/ { f = !a[$0]++ } f' aaaa.fa > bbbb.fa #count #fasta #oneliner

https://github.com/stephenturner/oneliners #Bash #Tutorial #OneLiner

Genome Mapping #OneLiner https://bioinformaticsonline.com/snippets/view/39310/one-liner-for-reads-mapping

Unmasking the lower case values in genome. $ perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna #Genome #Unmask #Perl #Oneliner

Rename/number the multi-fasta file in ascending order. $ awk '/^>/{print ">" ++i; next}{print}' < Mix_assembly.fasta > Mix_assembly2.fasta #awk #oneliner

Perl OneLiner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html #Perl #Oneliner #NGS #Script

NGS onliner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/subsetFASTAFASTAQ.html #OneLiner #NGS

Fasta sequence length: awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa #Length #Linux #OneLiner

Print all text after a matching string perl -ne "print unless 1 .. m(String)" #Perl #OneLiner #String #Perl #Trick

Count the number of sequences in fastaq file. grep -c '^@' sample1.fq #Fastaq #Count #Number #Grep #Dirty #Oneliner #NGS

Remove the fasta description and just keep the identifier. perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #Perl #Oneliner #Trick #Tips #Fasta #Identifier #Remove

Extract sequences by their ID from a fasta file. perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.txt sample1.fa #Extract #Sequences #IDs #Fasta #Perl #Trick #Oneliner

Fancy One-Liner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html #Perl #OneLiner #Bioinformatics #Quick #Common #Tricks #CommandLine #Terminal

Linux one-liner. https://wikis.utexas.edu/display/bioiteam/Scott%27s+list+of+linux+one-liners #Linux #Oneliner #NGS

Remove the blank space from a fasta file. perl -nlwe 'tr/ //d; print if length' fileName #Delete #Space #Fasta #Perl #Oneliner