Installation

Installation

Anaconda Installation

Installing on Linux https://docs.anaconda.com/anaconda/install/linux/

Note

  • Anaconda is installed in /opt directory .

JDK8 Installation [9]

  1. Download source pakage from Oracle. https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
  2. 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
  1. 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
  1. 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
  1. 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