raymondkiu / 16S_extraction_Barrnap

Automated 16S sequence extraction using Barrnap output gff files

16S rRNA sequence extraction from Barrnap outputs

Introduction

This is a simple automated Shell script that uses the Barrnap ribosomal RNA predictor (https://github.com/tseemann/barrnap) output gff files with 16S gene positions as input to extract single 16S rRNA sequence from original genome FASTA sequence files.

Usage

% ./16S_sequence_Barrnap.sh GFF FASTA

• Where GFF is the outputs from Barrnap and FASTA is the original FASTA sequence.
• This script will generate the final sequence file named FASTA-16S.fna, this should contain only single 16S sequence predicted by Barrnap - only the first 16S rRNA sequence predicted will be extracted using this script.

Dependencies

• samtools: http://www.htslib.org/
• bedtools: http://bedtools.readthedocs.io/en/latest/