Program name:	QC_pe.sh

Function:	Quality Control of Illumina PE Reads

Citation:	Chao Feng, Meizhen Xu, Chen Feng, Eric J. B. von Wettberg, Ming Kang. The complete chloroplast genome of Primulina and two novel strategies for development of high polymorphic loci for phylogenetic studies. BMC Evolutionary Biology 2017;

Author:	Chao Feng ([email protected])

Release date:	Jul. 15th, 2017

Version:	Version 1.0

Software:	Please make sure that FASTX_Toolkit ("http://hannonlab.cshl.edu/fastx_toolkit") have been installed and avaliable in your directory.

Preparation:	Put all the PE-end Reads (fq format), QC_pe.sh, QC_pe.pl and q2030.pl in the same folder. *two Read files should be named as $sample_raw.1.fq, $sample_raw.2.fq, respectively, e.g.: CZYX01-2_raw.1.fq, CZYX01-2_raw.2.fq.

Usage:	nohup sh QC_pe.sh $ThreadNumber $Read1_len $Read2_len >$Log 2>&1 &	
		$ThreadNumber: Max Thread can be used in this analysis.
		$Read1_len: the length of read1 in fastq file, e.g. 100.
		$Read2_len: the length of read2 in fastq file, e.g. 100.
		$Log: Record of output on the screen.
	E.g.: nohup sh QC_pe.sh 8 100 100 >Log.txt 2>&1 &

Note:	1) If your data was sequenced in order Illumina system with Phred64, please open the file q2030.pl, and exchange the number "53" and "63" in the line 21 and 24 into "84" and "94", respectively.
	2) This pipeline works on the fq file with the id line (line 1 of each 4 lines) which is combined with two parts, the former one is shared by both PE reads, the latter one has difference between PE reads. And these two parts are splited by black (" ") or tab ("	"), sush as @HWI-D00524:51:C587MANXX:4:1101:3260:1957 1:N:0:AGCAGT" or "@HWI-D00524:51:C587MANXX:4:1101:3260:1957 2:N:0:AGCAGT". Otherwise, this pipeline maybe not suitable for your data, we will adjust the pipeline if you email us.
	3) All the read1 or read2 in a fastq file used in this pipeline should have uniform length.

Output description:
	 $sample_1.fq and $sample_2.fq: the fq files after quality control.
	 $sample_1.fq.q2030 and $sample_2.fq.q2030: the stats files with the infomation of read No., Q20 and Q30 values.