Command line rRNASelector - 16S extraction

[susanklein]

Hi,

I need to extract all 16S sequences from a metagenome illumina run: 12 files of ~30M reads each (after qc). I have the java based rRNASelector, which uses hmmsarch and a custom database, it seems to be working but may take several hours per file. Does anyone know if there is a command line alternative so I can script this (rRNAselector is a GUI only).

Thanks,

S.

[WhatsOEver]

I never tried it, but "meta_rna" is a python script which is doing the things you are looking for (http://weizhong-lab.ucsd.edu/meta_rna/)

[susanklein]

Thanks, I'll give its a go. Distracted with something else now :/

S.

[yzzhang]

Based my knowledge, meta_rna is used for extracting rRNA feature from assembled contigs, not from raw reads, right?