text: user7405: I have hundreds of bacterial genomes and I would like to know which is the best informatic tool in which I can run all genomes on one go and get a 16S rRNA gene sequence of each genome as output.
  Could anyone give me some advice?
  
  user4282: You can use Barrnap
  barrnap -k bac --threads "$(nproc)" \
          -o output_rrna.fna < input_file.fna \
          > output_rrna.gff 2> /dev/null
  
  Put the file in one line of sequence per fasta id and get sequence with 16S annotation.
  perl -pe 'if(/\>/){s/\n/\t/}; s/\n//; s/\>/\n\>/' output_rrna.fa | \
      perl -pe 's/\t/\n/' | tail -n+2 | cut -d\: -f1 | \
      grep -A1 16S > output_16S.fasta
  
  Check the output_rrna.gff and make a BLAST of the sequence to be sure about the predicted 16S.
  
original_text: 7405: <p>I have hundreds of bacterial genomes and I would like to know which is the best informatic tool in which I can run all genomes on one go and get a 16S rRNA gene sequence of each genome as output.</p>
  
  <p>Could anyone give me some advice?</p>
   4282: <p>You can use <a href="https://github.com/tseemann/barrnap" rel="nofollow noreferrer">Barrnap</a></p>
  
  <pre><code>barrnap -k bac --threads "$(nproc)" \
          -o output_rrna.fna &lt; input_file.fna \
          &gt; output_rrna.gff 2&gt; /dev/null
  </code></pre>
  
  <p>Put the file in one line of sequence per fasta id and get sequence with 16S annotation.</p>
  
  <pre><code>perl -pe 'if(/\&gt;/){s/\n/\t/}; s/\n//; s/\&gt;/\n\&gt;/' output_rrna.fa | \
      perl -pe 's/\t/\n/' | tail -n+2 | cut -d\: -f1 | \
      grep -A1 16S &gt; output_16S.fasta
  </code></pre>
  
  <p>Check the <code>output_rrna.gff</code> and make a BLAST of the sequence to be sure about the predicted 16S.</p>
  