基因组分析

bwa

安装

git clone https://github.com/lh3/bwa.git
cd bwa
make

使用

bwa index MY3.fasta
bwa mem -t 4 MY3.fasta /home/llt/experiment/data/clean/trim_strict/ssg1_2m.1.fq /home/llt/experiment/data/clean/trim_strict/ssg1_2m.2.fq > ssg1_2m.sam

Samtools

安装

git clone https://github.com/samtools/htslib.git
cd htslib
autoheader 
autoconf 
./configure 
make
make install
git clone https://github.com/samtools/samtools.git
cd samtools
autoheader
autoconf -Wno-syntax
./configure
make
make install

使用

samtools view -bS -1 ssg1_2m.sam > ssg1_2m.bam
samtools sort -@ 4 -O bam -o ssg1_2m.sorted.bam ssg1_2m.bam
samtools index ssg1_2m.sorted.bam

Picard

安装

git clone https://github.com/broadinstitute/picard.git
cd picard/
wget https://downloads.gradle.org/distributions/gradle-5.2-all.zip
unzip gradle-5.2-all.zip
export PATH=$PATH:/home/llt/software/gradle-5.2/bin
chmod 777 /home/llt/software/gradle-5.2/bin/gradle
gradle -v
wget https://download.oracle.com/otn-pub/java/jdk/8u201-b09/42970487e3af4f5aa5bca3f542482c60/jdk-8u201-linux-x64.tar.gz?AuthParam=1549373804_a0a6f48a0b24ae3c8af2b42117df1221
mv jdk-8u201-linux-x64.tar.gz\?AuthParam\=1549373804_a0a6f48a0b24ae3c8af2b42117df1221 jdk-8u201-linux-x64.tar.gz
tar -zxvf jdk-8u201-linux-x64.tar.gz
vim /etc/profile 
export JAVA_HOME=/usr/local/jdk1.8
export JRE_HOME=${JAVA_HOME}/jre
export CLASSPATH=.:${JAVA_HOME}/lib:${JRE_HOME}/lib
export PATH=.:${JAVA_HOME}/bin:$PATH
source /etc/profile 
java -version
./gradlew shadowJar

使用

java -jar /home/llt/software/picard/build/libs/picard.jar MarkDuplicates I=ssg1_2m.sorted.bam O=ssg1_2m.sorted.markdup.bam M=ssg1_2m.markdup_metrics.txt
samtools index ssg1_2m.sorted.markdup.bam