一、安装配置JDK环境

1.通过源安装

sudo apt install openjdk-10-jdk
java -version

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2.从官网下载安装包安装

mkdir ~/Biosofts
sudo mkdir /usr/java
sudo tar -zvxf /media/sf_Linux/Biosoft/jdk-8u172-linux-x64.tar.gz -C /usr/java/
sudo cd /usr/java
sudo ln -s jdk1.8.0_172 latest
sudo ln -s /usr/java/latest default
sudo vi /etc/profile
#末尾加上如下几行
export JAVA_HOME=/usr/java/latest
export PATH=$JAVA_HOME/bin:$JAVA_HOME/jre/bin:$PATH
export CLASSPATH=.:$JAVA_HOME/lib/dt.jar:$JAVA_HOME/lib/tools.jar
source /etc/profile
java -version

二、序列数据质量控制

1.FastQC安装

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip
mkdir ~/Biosofts/fastqc
unzip /media/sf_Linux/Biosoft/fastqc_v0.11.7.zip -d ~/Biosofts/
~/Biosofts/FastQC/fastqc -h
echo 'export PATH=~/Biosofts/FastQC:$PATH' >>~/.bashrc
source ~/.bashrc
fastqc -h

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2.FastQC使用

fastqc SRR6937757_1.fastq.gz

结果：生成html文件

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3.Trimmomatic安装与使用

Trimmomatic用来切除接头序列和低质量碱基

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
unzip Trimmomatic-0.38.zip -d ~/Biosofts/Trimmomatic038/

运行：

java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar SE -phred33 SRR6937757_1.fastq.gz ./out1.fq.gz  ILLUMINACLIP:/home/lky/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:75

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处理后序列FastQC：

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单末端测序模式

java -jar <path to trimmomatic jar> SE [-threads <threads>] [-phred33 | -phred64] [-trimlog
<logFile>] <input> <output> <step 1> <step 2> ...

双末端测序模式

java -jar <path to trimmomatic.jar> PE [-threads <threads] [-phred33 | -phred64] [-trimlog
<logFile>] >] [-basein <inputBase> | <input 1> <input 2>] [-baseout <outputBase> |
<paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> <step 2>

参数解析见：http://www.biotrainee.com/