sickle

对测序数据进行质控时，通常考虑三点：

1.quality trimming

2.adapter removal

3.contaminant filtering

除杂时我们用到了sickle，它能去除低质量的reads还能保证双端序列的完整性

下载地址：

https://github.com/najoshi/sickle

 安装步骤：

cd ~/biosoft mkdir sickle && cd sickle  #建立文件夹

wget https://codeload.github.com/najoshi/sickle/zip/master -O sickle.zip   #进行下载

unzip sickle.zip                    #解压

cd sickle-master

make                 #编译

~/biosoft/sickle/sickle-master/sickle -h           #查看帮助

命令语句：

~/biosoft/sickle/sickle-master/sickle pe -f test1.fastq -r test2.fastq -t sanger -o trimmed_output_file1.fastq -p trimmed_output_file2.fastq

使用参数：

pe : use paired-end mode 
-f training/rnaseq/ERR022486_chr22_read1.fastq.gz : the fastq file for read 1 
-r training/rnaseq/ERR022486_chr22_read2.fastq.gz : the fastq file for read 2 
-t sanger : the quality encoding. All data downloaded from EBI or NCBI will be "sanger" encoded. For an explanation: 
-o ERR022486_chr22_read1_trim.fastq : the output file for trimmed reads from read 1 
-p ERR022486_chr22_read2_trim.fastq : the output file for trimmed reads from read 2 
-s ERR022486_chr22_single_trim.fastq : the output file for reads where the mate has failed the quality or length filter 
-q 30 : the quality value to use. Bases below this will be trimmed, using a sliding window 
-l 15 : the minimum length allowed after trimming. Here we remove reads with less than 15bp

给出的结果格式：

参考：https://www.jianshu.com/p/849dcf25d840