What method do you recommend to extract 16S sequences from whole metagenome data?

Hi
I have two whole metagenome data, also ORF.fasta file i want to separate the 16S marker gene sequence and to analysis in qiime, is their and code available.
Thank you for your valuable time

Hi @kulandai1,
I have reclassified this post as “other bioinformatics tools” since this is not really a QIIME 2 question, but about other methods unrelated to QIIME 2 (even though it sounds like eventually you want to input these data into QIIME 2).

You could try SortMeRNA, it’s one tool I can think of designed for this very purpose: https://github.com/biocore/sortmerna