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I have a DNA sequence for which I would like to quickly find the reverse complement. Is there a quick way of doing this on the bash command line using only GNU tools?

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3 Answers 3

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Thanks to Manu Tamminen for this solution:

echo ACCTTGAAA | tr ACGTacgt TGCAtgca | rev
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  • $\begingroup$ And if I want to put it into a variable instead of echo it? $\endgroup$
    – Adi Ro
    Commented Jan 6, 2020 at 9:44
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    $\begingroup$ I would enclose the code in $() and assign to a variable assuming you are using a recent version of bash. $\endgroup$
    – winni2k
    Commented Jan 6, 2020 at 11:35
  • $\begingroup$ that works thanks! $\endgroup$
    – Adi Ro
    Commented Jan 9, 2020 at 9:29
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Reverse complement FASTA/Q:

seqtk seq -r in.fa > out.fa

https://github.com/lh3/seqtk

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You may either install the emboss package (http://emboss.sourceforge.net/download/) and use the revseq program. It contains many useful command-line programs such as the pairwise alignment tool needle.

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