how i can recover the 16S from a set of FASTA files. is there any script or utility that does that and thanks in advance
What's your input? shotgun metagenomics? 16S amplicon?
input : scaffold.fasta
yes for 16S
What did you assemble and how? You can annotate it with prokka and get the rRNA but the reliability depends on the assmebly
Have a look at Barrnap and RNAmmer.
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