Looking for a tool to find 16S rRNA in hundreds of genomes 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?
You can use Barrnap

barrnap -k bac --threads "$(nproc)" \
        -o output_rrna.fna &lt; input_file.fna \
        &gt; output_rrna.gff 2&gt; /dev/null


Put the file in one line of sequence per fasta id and get sequence with 16S annotation.

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


Check the output_rrna.gff and make a BLAST of the sequence to be sure about the predicted 16S.