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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?

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    $\begingroup$ Have you tried anything any particular? As a general rule, there is no single "best" tool for much of anything, you just need something to give you a reliable result. $\endgroup$
    – Devon Ryan
    Feb 23, 2020 at 23:32

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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.

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  • $\begingroup$ Thanks zorbax, I am going to have a look and I will give you a comment about what I get $\endgroup$ Feb 25, 2020 at 11:30
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You can perform genome annotation using tools like prokka or PGAP. Using some python scripts you can extract the predicted 16S and blast to confirm.

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