#!/bin/bash
#Author: Renato Oliveira
#version: 1.0
#Date: 02-05-2023

###    Copyright (C) 2023  Renato Oliveira
###
###    This program is free software: you can redistribute it and/or modify
###    it under the terms of the GNU General Public License as published by
###    the Free Software Foundation, either version 3 of the License, or
###    any later version.
###
###    This program is distributed in the hope that it will be useful,
###    but WITHOUT ANY WARRANTY; without even the implied warranty of
###    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
###    GNU General Public License for more details.
###
###    You should have received a copy of the GNU General Public License
###    along with this program.  If not, see <http://www.gnu.org/licenses/>.

###Contacts:
###    renato.renison@gmail.com

SAMPLE="ITV10661"


#Quality Treatment with  AdapterRemoval
AdapterRemoval --file1 ${SAMPLE}_R1.fastq --file2 ${SAMPLE}_R2.fastq --threads 10 --mate-separator ' ' --adapter-list adapter.txt \
	--trimwindows 10 --minquality 20 --minlength 70 --basename ${sample}_good -mm 5


#Assembling with NovoPlasty 3.6
perl NOVOPlasty3.6.pl -c config.txt