Hi everyone, I got some binning data and I want to retrieve 16s sequences from them. The binning data are supposed to be pure single genome, but each of them is composed of several contigs. So it may cause problem if I submit them to 16sr RNA identifier like RNAmmer which requires single genome sequence file. Do you know any program serves this purpose? Many thanks:)~
BBDuk works well for this purpose, if you have a large set of curated ribosomal sequences (such as Silva). You can run it on the reads or the assemblies.
bbduk.sh in=data.fa outm=ribo.fa outu=nonribo.fa k=31 ref=silva.fasta
Though, I'm not quite clear why you want to remove the 16S...
hmm_RNA uses hidden Markov models to find SSU and LSU on metagenomic assemblies. It is sensitive, finding even small fragments on draft assemblies, but its identification is inaccurate, calling "Archeal" or "Eukariotic" several bacterial sequences.