Installation¶
Installation¶
Anaconda Installation¶
Installing on Linux https://docs.anaconda.com/anaconda/install/linux/
Note
- Anaconda is installed in
/opt
directory .
JDK8 Installation [9]¶
- Download source pakage from Oracle. https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
- Extract JDK8 files to the target folder.
sudo mkdir /usr/lib/jvm
sudo tar -zxvf jdk-8u211-linux-x64.tar.gz -C /usr/lib/jvm
- Set environment variables for JDK8.
sudo nano ~/.bashrc
#set oracle jdk environment
export JAVA_HOME=/usr/lib/jvm/jdk-1.8.0_211
export JRE_HOME=${JAVA_HOME}/jre
export CLASSPATH=.:${JAVA_HOME}/lib:${JRE_HOME}/lib
export PATH=${JAVA_HOME}/bin:$PATH
#make changes take effect immediately
source ~/.bashrc
- Set JDK8 to jdk-1.8.0_211.
sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/jdk-1.8.0_211/bin/java 300
sudo update-alternatives --install /usr/bin/javac javac /usr/lib/jvm/jdk-1.8.0_211/bin/javac 300
sudo update-alternatives --install /usr/bin/jar jar /usr/lib/jvm/jdk-1.8.0_211/bin/jar 300
sudo update-alternatives --install /usr/bin/javah javah /usr/lib/jvm/jdk-1.8.0_211/bin/javah 300
sudo update-alternatives --install /usr/bin/javap javap /usr/lib/jvm/jdk-1.8.0_211/bin/javap 300
#set path to jdk-1.8.0_211
sudo update-alternatives --config java
- Test
java -version
# The following messages should be showed if it works.
java version "1.8.0_211"
Java(TM) SE Runtime Environment (build 1.8.0_211-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.211-b12, mixed mode)
Guppy Installation¶
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features. [1]
wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_3.0.3_linux64.tar.gz
tar -xf ont-guppy-cpu_3.0.3_linux64.tar.gz
sudo mv ont-guppy-cpu_3.0.3_linux64 /opt/ont-guppy-cpu_3.0.3
Porechop Installation¶
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. [2]
/opt/anaconda3/bin/conda create -n porechop
source /opt/anaconda3/bin/activate porechop
conda install -c bioconda porechop
conda deactivate
NanoStat Installation¶
NanoStat calculates various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format. [3]
/opt/anaconda3/bin/conda create -n nanostat
source /opt/anaconda3/bin/activate nanostat
conda install -c bioconda nanostat
conda deactivate
NanoFilt Installation¶
NanoFilt filters and trims long read sequencing data. [4]
/opt/anaconda3/bin/conda create -n nanofilt
source /opt/anaconda3/bin/activate nanofilt
conda install -c bioconda nanofilt
conda deactivate
Unicycler Installation¶
Unicycler is an assembly pipeline for bacterial genomes. [5]
/opt/anaconda3/bin/conda create -n unicycler
source /opt/anaconda3/bin/activate unicylcer
conda install -c bioconda unicycler
conda install -c bioconda bcftools # for .vcf file
conda deactivate
Warning
- Change the memory setting in Pilon is necessary or it could be failed to start [10] .
BUSCO Installation¶
BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9. [6]
/opt/anaconda3/bin/conda create -n busco
source /opt/anaconda3/bin/activate busco
conda install -c bioconda busco
conda deactivate
BWA Installation¶
BWA is a software package for mapping low-divergent sequences against a large reference genome. [7]
/opt/anaconda3/bin/conda create -n bwa
source /opt/anaconda3/bin/activate bwa
conda install -c bioconda bwa
conda deactivate
Seqtk Installation¶
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. [8]
/opt/anaconda3/bin/conda create -n seqtk
source /opt/anaconda3/bin/activate seqtk
conda install -c bioconda seqtk
conda deactivate
Trimmomatic Installation¶
Trimmomatic is a flexible read trimming tool for Illumina NGS data. [11]
/opt/anaconda3/bin/conda create -n trimmomatic
source /opt/anaconda3/bin/activate trimmomatic
conda install -c bioconda trimmomatic
conda deactivate
[1] | Guppy v3.0.3 Release https://community.nanoporetech.com/posts/guppy-3-0-release |
[2] | Porechop https://github.com/rrwick/Porechop |
[3] | NanoStat https://github.com/wdecoster/nanostat |
[4] | NanoFilt https://github.com/wdecoster/nanofilt |
[5] | Unicycler https://github.com/rrwick/Unicycler |
[6] | BUSCO v3 https://busco.ezlab.org |
[7] | BWA https://github.com/lh3/bwa |
[8] | Seqtk https://github.com/lh3/seqtk |
[9] | Ubuntu 安装 JDK 7 / JDK8 的两种方式 https://www.cnblogs.com/a2211009/p/4265225.html |
[10] | Pilon step runs out of error https://github.com/rrwick/Unicycler/issues/147 |
[11] | Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic |