What is a quick way to find the reverse complement in bash

Question

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?

score 32 · Accepted Answer · edited Apr 15 '19 at 14:03

32

Thanks to Manu Tamminen for this solution:

echo ACCTTGAAA | tr ACGTacgt TGCAtgca | rev

edited Apr 15 '19 at 14:03

Chris_Rands

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answered Apr 15 '19 at 09:46

winni2k

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And if I want to put it into a variable instead of echo it? – Adi Ro Jan 06 '20 at 09:44
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I would enclose the code in $() and assign to a variable assuming you are using a recent version of bash. – winni2k Jan 06 '20 at 11:35
that works thanks! – Adi Ro Jan 09 '20 at 09:29

score 7 · Answer 2 · answered Oct 01 '20 at 14:30

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Reverse complement FASTA/Q:

seqtk seq -r in.fa > out.fa

https://github.com/lh3/seqtk

answered Oct 01 '20 at 14:30

user9619

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score 2 · Answer 3 · answered Apr 29 '20 at 09:02

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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.

answered Apr 29 '20 at 09:02

thomas duge de bernonville

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What is a quick way to find the reverse complement in bash

3 Answers3