#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=48g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL


module load QIIME2/2019.7

rawdir=/data/mramseylab/raw_reads/2023_SUPP_V1V2
visdir=/data/mramseylab/visualizations/AL_2023
metadata=/data/mramseylab/metadata/plaque_meta_5.tsv

qiime quality-filter q-score-joined \
--i-demux $rawdir/demux-v1v2-master.qza \
--p-min-quality 20 \
--o-filtered-sequences $rawdir/demux-v1v2-q20.qza

qiime demux summarize \
--i-data $rawdir/demux-v1v2-q20.qza \
--o-visualization $visdir/demux-v1v2-q20.qzv