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Extract fasta with pattern $ perl -n -e '$on=(/^>(A)/) if (/^>/); print $_ if ($on);' pilonCor_round1.fasta > A_set.fa #Pattern #Extract #Fasta

#Extract all the files from a #directory and #sub-dir with #pattern. $ find TrimmedDir -type f | grep "L_" | xargs -i cp {} .

Find matching file names with pattern in a directory. $ ls -dq *_name2search_* | wc -l #file #search #hits #pattern #names #directory

Find a pattern in first 7 characters of reads. bioawk -c fastx 'substr($seq,0,7) == $TAG { print }' reads.fq.gz #Reads #NGS #Extract #Pattern

Print all the values beetween a pattern "abc" > awk '/abc/{flag=1;next}/mno/{flag=0}flag' file #awk #print #range #pattern

Search a PATTERN in a file and print the line. perl -ne '/PATTERN/ && print' fileName #Perl #Pattern #Print #Search #Line

Suffix Trees ! http://www.cs.cmu.edu/~ckingsf/bioinfo-lectures/suffixtrees.pdf #SuffixTree #Pattern