安装代码如下：

## https://github.com/najoshi/sickle
cd ~/biosoft
mkdir sickle && cd sickle
wget https://codeload.github.com/najoshi/sickle/zip/master -O sickle.zip
unzip sickle.zip
cd sickle-master
make
~/biosoft/sickle/sickle-master/sickle -h

这个软件很简单，就是去除低质量的reads，而且还可以保证双端测序的完整性。

本实例的测试数据可以在 http://www.biotrainee.com/jmzeng/reads/test1.fastq   和 http://www.biotrainee.com/jmzeng/reads/test2.fastq 

这个软件支持gz压缩格式，我应该压缩好了再上传到我们的云服务器的，这样可以节省流量，这只是一个测试，如果数据传输压力太大了，我们可能会取消链接，改为百度云分享！
~/biosoft/sickle/sickle-master/sickle pe -f test1.fastq -r test2.fastq -t sanger -o trimmed_output_file1.fastq -p trimmed_output_file2.fastq

软件给出的log日志如下：

PE forward file: test1.fastq
PE reverse file: test2.fastq

Total input FastQ records: 200000 (100000 pairs)

FastQ paired records kept: 192262 (96131 pairs)
FastQ single records kept: 3869 (from PE1: 3864, from PE2: 5)
FastQ paired records discarded: 0 (0 pairs)
FastQ single records discarded: 3869 (from PE1: 5, from PE2: 3864)

然后批量查看处理前后的fastqc质量报告：
ls *fastq |xargs -P 5 ~/biosoft/fastqc/FastQC/fastqc

比较所有的fastq文件的结果报告就可以看出它做了什么！

sickle处理前后的结果文件都可以在 http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip 下载。

当然，这只是默认参数的用法，还可以添加很多参数! 比如   -q 30 -l 15 参数解释如下：

• 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:http://en.wikipedia.org/wiki/FASTQ_format#Encoding

• -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