NGS Tools | Installation

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FastQc

Download Link :-
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip

Installation :-

Extract fastqc_v0.11.7.zip

Open bash.bashrc with

                                                        
                                                            
                                                                
                                                                    sudo
                                                                
                                                                gedit /etc/bash.bashrc

edit bash.bashrc file with "< / PATH for Extracted Folder>/FastQC/ "

                                                        
                                                            
                                                                                                                        
                                                                
                                                                 
                                                                    export PATH=$PATH:< / PATH for Extracted Folder>/FastQC/

To edit the Permission for the fastqc

                                                        
                                                            
                                                                      
                                                                    sudo                                                  
                                                                
                                                                 
                                                                    chmod -R 777 < / PATH for Extracted Folder>/FastQC/

To Install Java Runtime Environment

                                                        
                                                            
                                                                      
                                                                    sudo apt-get install                                               
                                                                
                                                                 
                                                                    default-jre

Cutadapt

Download Link :-
NA

Installation :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo apt-get install                                               
                                                                
                                                                 
                                                                    python-cutadapt

(OR)

                                                        
                                                            
                                                                      
                                                                    sudo apt-get install                                               
                                                                
                                                                 
                                                                    cutadapt

R-base

Download Link :-
NA

Installation :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo apt-get install
                                                                
                                                                
                                                                    r-base

R-studio

Download Link :-
https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb

Installation :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo 
                                                                
                                                                
                                                                    dpkg -i rstudio-xenial-1.1.456-amd64.deb

If the command is giving Error

                                                        
                                                            
                                                                      
                                                                    sudo 
                                                                
                                                                
                                                                    apt-get install -f

1 : Samtools

install the required packages :-

gcc

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install gcc

zlib1g-dev

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install zlib1g-dev

htslib
Download Link :-
https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2

libbz2-dev

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install libbz2-dev

Download Link of samtools :-

https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2

                                                        
                                                            
                                                                      
                                                                
                                                                
                                                                    cd samtools-1.9

                                                            
                                                                
                                                                          
                                                                    
                                                                    
                                                                        ./configure –prefix=/where/to/install

Make Install

Add the installed path to the bash.bashrc file

                                                        
                                                            
                                                                      
                                                                
                                                                
                                                                    export PATH=$PATH:/< PATH for Extracted Folder>/samtools-1.9

2 : BWA

Download Link :-
https://sourceforge.net/projects/bio-bwa/files/latest/download?source=typ_redirect

download, extract them and Add the path in the "/etc/bash.bashrc file"

(OR)

For Installation via terminal :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo                                              
                                                                
                                                                 
                                                                    apt-get install bwa

3 : Tophat2

Download Link :-
http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz

download, extract them and Add the path in the "/etc/bash.bashrc file"

(OR)

For Installation via termianal :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo                                              
                                                                
                                                                 
                                                                    apt-get install tophat

4 : Bowtie

Download Link :-
https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip/download

download, extract them and Add the path in the "/etc/bash.bashrc file"

(OR)

For Installation via termianal :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo                                              
                                                                
                                                                 
                                                                    apt-get install bowtie

5 : cufflinks

Download Link :-
http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz

download, extract them and Add the path in the "/etc/bash.bashrc file"

6 : IGV

Download Link :-
http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.13.zip

download, extract them and Add the path in the "/etc/bash.bashrc file"

1 : Trinity

Install the required packages :-

bowtie2
Download Link :-
http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.13.zip
download, extract them and Add the path in the "/etc/bash.bashrc file"

jellyfish

Installation

                                                                
                                                                    
                                                                        
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install jellyfish

salmon

Download the Binaries :-
http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.13.zip
download, extract them and Add the path in the "/etc/bash.bashrc file"

Extract the folder :-

                                                                        
                                                                            
                                                                                      
                                                                                
                                                                                
                                                                                    tar -xzf salmon-0.11.2-linux_x86_64 salmon-0.11.2-linux_x86_64.tar.gz

                                                                        
                                                                            
                                                                                      
                                                                                                                                                    
                                                                                
                                                                                    cd salmon-0.11.2-linux_x86_64

copy “salmon-0.11.2-linux_x86_64/bin/salmon” and paste at
“/home/arraygen/Videos/sw/Trinityrnaseq-v2.6.6/trinity-plugins/BIN/”
copy “salmon-0.11.2-linux_x86_64/lib” and paste at
“/home/arraygen/Videos/sw/Trinityrnaseq-v2.6.6/trinity-plugins/”

Inchworm *
Chrysalis *
QuantifyGraph *
GraphFromFasta *
ReadsToTranscripts *
parafly *

boost

Installation :-

                                                                
                                                                    
                                                                          
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install libboost-dev

( * will be installed, when running the “sudo make”)

Plugings

slclust ^
collectl ^
(^ will be installed, when running the “sudo make plugins”)
Download Link :-
https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.6.6/Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz

Extarct the Folder

                                                                        
                                                                            
                                                                                  
                                                                                
                                                                                
                                                                                    tar -xzf Trinity-v2.6.6 Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz

Change the directory

                                                                        
                                                                            
                                                                                  
                                                                                
                                                                                
                                                                                    cd  Trinity-v2.6.6

                                                                        
                                                                            
                                                                                  
                                                                                    sudo
                                                                                
                                                                                
                                                                                    make plugins

2 : Transdecoder

Download Link :-
https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.3.0.tar.gz

Installation :-

Extract TransDecoder-v5.3.0.tar.gz

                                                        
                                                            
                                                                
                                                                
                                                                
                                                                    tar -xzf TransDecoder-v5.3.0 TransDecoder-v5.3.0.tar.gz

Download, extract them and Add the path in the "/etc/bash.bashrc file" run with :-

                                                        
                                                            
                                                                                                                        
                                                                
                                                                 
                                                                    ./TransDecoder.LongOrfs

                                                        
                                                            
                                                                                                                        
                                                                
                                                                 
                                                                    ./TransDecoder.Predict

3 : BLAST

Installation :-

Open Terminal and type the below command

                                                        
                                                            
                                                                
                                                                    sudo apt-get install 
                                                                
                                                                
                                                                    ncbi-blast+

after installaion we can check blast in the terminal

4 : bowtie2

Download Link :-
https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip/download

Download, extract them and Add the path in the "/etc/bash.bashrc file"

Installation :-

Open Terminal and type the below command

                                                        
                                                            
                                                                
                                                                    sudo apt-get install 
                                                                
                                                                
                                                                bowtie

(OR)

                                                        
                                                            
                                                                
                                                                    sudo apt-get install 
                                                                
                                                                
                                                                    bowtie2

after installaion we can check blast in the terminal

5 : EdgeR

R-base

Download Link :-
NA

Installation :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo apt-get install
                                                                
                                                                
                                                                    r-base

R-studio

Download Link :-
https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb

Installation :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo 
                                                                
                                                                
                                                                    dpkg -i rstudio-xenial-1.1.456-amd64.deb

If the command is giving Error

                                                        
                                                            
                                                                      
                                                                    sudo 
                                                                
                                                                
                                                                    apt-get install -f

In the R Studio run this commands

                                                        
                                                            
                                                                      
                                                                
                                                                
                                                                    source("https://bioconductor.org/biocLite.R")

                                                        
                                                            
                                                                      
                                                                
                                                                
                                                                    biocLite("edgeR")

1 : Samtools

install the required packages :-

gcc

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install gcc

zlib1g-dev

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install zlib1g-dev

htslib
Download Link :-
https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2

libbz2-dev

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install libbz2-dev

Download Link of samtools :-

https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2

                                                            
                                                                
                                                                          
                                                                    
                                                                    
                                                                        cd samtools-1.9

                                                            
                                                                
                                                                          
                                                                    
                                                                    
                                                                        ./configure –prefix=/where/to/install

Make Install

Add the installed path to the bash.bashrc file

                                                        
                                                            
                                                                      
                                                                
                                                                
                                                                    export PATH=$PATH:/< PATH for Extracted Folder>/samtools-1.9

2 : snpEFF

Download Link :-
https://sourceforge.net/projects/snpeff/files/latest/download?source=files

Download, extract them

run as

                                                            
                                                                
                                                                          
                                                                    
                                                                     
                                                                        jar snpEff.jar

3 : BWA

Download Link :-
https://sourceforge.net/projects/bio-bwa/files/latest/download?source=typ_redirect

download, extract them and Add the path in the "/etc/bash.bashrc file"

(OR)

For Installation via terminal :-

Open Terminal and type the following command :-

                                                            
                                                                
                                                                          
                                                                        sudo                                              
                                                                    
                                                                     
                                                                        apt-get install bwa

4 : IGV

Download Link :-
http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.13.zip

download, extract them and Add the path in the "/etc/bash.bashrc file"

1 : Trimmomatic

Download Link :-
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip

Download, extract them

run as

                                                        
                                                            
                                                                      
                                                                
                                                                 
                                                                    jar trimmomatic-0.38.jar

2 : BisMark Tool

Download Link :-
https://github.com/FelixKrueger/Bismark/archive/master.zip

download, extract them and Add the path in the "/etc/bash.bashrc file"

Bismark requires

Bowtie2 or Bowtie1

Samtools

3 : MethylKit

R-base

Download Link :-
NA

Installation :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo apt-get install
                                                                
                                                                
                                                                    r-base

R-studio

Download Link :-
https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb

Installation :-

Open Terminal and type the following command :-

                                                        
                                                            
                                                                      
                                                                    sudo 
                                                                
                                                                
                                                                    dpkg -i rstudio-xenial-1.1.456-amd64.deb

If the command is giving Error

                                                        
                                                            
                                                                      
                                                                    sudo 
                                                                
                                                                
                                                                    apt-get install -f

In the R Studio run this commands

                                                        
                                                            
                                                                      
                                                                
                                                                
                                                                source("https://bioconductor.org/biocLite.R")

                                                        
                                                            
                                                                      
                                                                
                                                                
                                                                    biocLite("methylKit")

1 : Mirdeep2

Download Link :-
https://github.com/rajewsky-lab/mirdeep2/archive/master.zip

Download, extract them

Run

                                                        
                                                            
                                                                   
                                                                    sudo   
                                                                
                                                                 
                                                                    perl install.pl

It will download install the dependent packages

bowtie1.1.8
RNAfold
randfold
make_html.pl

It will requires a perl module “PDF::API2”

PDF::API2 perl module can be installed using cpan
run:

                                                        
                                                            
                                                                   
                                                                
                                                                 
                                                                    cpan https://github.com/rajewsky-lab/mirdeep2/archive/master.zip
                                                                
                                                                
                                                            
                                                        
                                                        (give “yes” to configure automatically.)

At cpan shell :-

                                                        
                                                            
                                                                  
                                                                
                                                                 
                                                                install PDF::API2

After installation exit the cpan. & check the programm with the test data.

                                                        
                                                            
                                                                  
                                                                
                                                                 
                                                                    sh /mirdeep2-master/tutorial_dir/run_tut.sh

1 : BLAST

Installation :-

Open Terminal and type the below command

                                                        
                                                            
                                                                
                                                                    sudo apt-get install 
                                                                
                                                                
                                                                    ncbi-blast+

after installaion we can check blast in the terminal

2 : QIIME (Quantitative Insights Into Microbial Ecology)

qiime requires python-pip version 10.01

Check pip version by
Open Terminal and type the below command

If you have pip 10.0.1 or more proceed with installation of Qiime, if not upgrade pip

                                                        
                                                            
                                                                
                                                                    sudo                                                      
                                                                
                                                                 
                                                                    pip install pip==10.0.1

Installation of miniconda

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    mkdir -p ~/miniconda3

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    ~/miniconda3/miniconda.sh

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    rm -rf ~/miniconda3/miniconda.sh

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    mkdir -p ~/miniconda3

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    ~/miniconda3/miniconda.sh

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    rm -rf ~/miniconda3/miniconda.sh

After installing, initialize your newly-installed Miniconda. The following commands initialize for bash and zsh shells:

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                ~/miniconda3/bin/conda init bash

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    ~/miniconda3/bin/conda init zsh

QIIME INSTALLATION STEPS

In your Terminal (on Windows, switch to WSL), download the configuration file for a Conda environment that also contains QIIME 2

                                                                
                                                                    
                                                                        
                                                                        
                                                                         
                                                                            "https://data.qiime2.org/distro/core/qiime2-2020.8-py36-linux-conda.yml" > \

                                                                
                                                                    
                                                                        
                                                                        
                                                                         
                                                                            "qiime2.yml"

Create a new Conda environment (this also installs QIIME 2):

                                                                
                                                                    
                                                                        
                                                                        
                                                                         
                                                                            conda env create -n qiime2 --file qiime2.yml

Delete the environment configuration file:

                                                                
                                                                    
                                                                        
                                                                        
                                                                         
                                                                            rm qiime2.yml

Activate the new Conda environment we have created:

                                                                
                                                                    
                                                                        
                                                                        
                                                                         
                                                                            conda activate qiime2

(OR)

Installation of Qiime to install other required packages such as “build-essential” “python-dev”

                                                        
                                                            
                                                                
                                                                    sudo apt-get install 
                                                                
                                                                 
                                                                    build-essential python-dev python2.7-setuptools-git

                                                        
                                                            
                                                                
                                                                    sudo apt-get install 
                                                                
                                                                 
                                                                    python-tk

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    pip install numpy

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    pip install scikit-bio==0.2.3

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    pip install qiime

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    pip install XlsxWriter

After installing the QIIME base packages, you can test the installation

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    print_qiime_config.py -t

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    pick_otus.py -h

3 : Samtools

install the required packages :-

gcc

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install gcc

zlib1g-dev

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install zlib1g-dev

htslib
Download Link :-
https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2

libbz2-dev

                                                                
                                                                    
                                                                              
                                                                            sudo 
                                                                        
                                                                        
                                                                            apt-get install libbz2-dev

Download Link of samtools :-

https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2

                                                            
                                                                
                                                                          
                                                                    
                                                                    
                                                                        cd samtools-1.9

                                                            
                                                                
                                                                          
                                                                    
                                                                    
                                                                        ./configure –prefix=/where/to/install

Make Install

Add the installed path to the bash.bashrc file

                                                        
                                                            
                                                                      
                                                                
                                                                
                                                                    export PATH=$PATH:/< PATH for Extracted Folder>/samtools-1.9

4 : Clustalw

Installation :-

Open Terminal and type the below command

                                                        
                                                            
                                                                
                                                                    sudo apt-get install 
                                                                
                                                                
                                                                    clustalw

To check the installtion run:

5 : Phylip

Installation :-

Open Terminal and type the below command

                                                        
                                                            
                                                                
                                                                    sudo apt-get install 
                                                                
                                                                
                                                                    phylip

To check the installtion run:

6 : hisat2

Download Link

git clone https://github.com/DaehwanKimLab/hisat2.git

make

anaconda:

                                                        
                                                            
                                                                
                                                                
                                                                
                                                                    bash Anaconda3-2022.05-Linux-x86_64.sh
                                                                
                                                                
                                                            
                                                        
                                                        (enter>>yes>.yes>)

                                                        
                                                            
                                                                
                                                                
                                                                 
                                                                    home/arraygen/bash/activate

7 : HTSEQ

Download Link

https://github.com/htseq/htseq#readme

(download htseq from code section)

                                                        
                                                            
                                                                
                                                                
                                                                
                                                                    https://shicheng-guo.github.io/research/1941/01/08/HTseq

To use HTSeq, you need Python 3.7 or above with:

NumPy, a commonly used Python package for numerical calculations
Pysam, a Python interface to samtools.
To make plots you will need matplotlib, a plotting library.

To check the python vesion and install the modules :-

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install matplotlib

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install Cython

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install pysam

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install swig

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install deeptoolsintervals

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install numpydoc

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install py2bit

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install pyBigWig

                                                                    
                                                                        
                                                                            
                                                                            
                                                                            
                                                                                pip install scipy

                                                        
                                                            
                                                                
                                                                
                                                                
                                                                    pip install HTSeq

For Error reffer this :-

https://askubuntu.com/questions/1276852/e-package-python-scipy-has-no-installation-candidate-ubuntu-20-04

8 : ragout

Download Link

https://anaconda.org/bioconda/ragout

                                                        
                                                            
                                                                
                                                                
                                                                
                                                                    conda install -c bioconda ragout

                                                        
                                                            
                                                                
                                                                
                                                                
                                                                    conda install -c bioconda/label/cf201901 ragout

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NGS TOOLS INSTALLATION

FastQc

FastQc

FastQc

Download Link :- https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip

Installation :-

Extract fastqc_v0.11.7.zip

Open bash.bashrc with

edit bash.bashrc file with "< / PATH for Extracted Folder>/FastQC/ "

To edit the Permission for the fastqc

To Install Java Runtime Environment

Cutadapt

Cutadapt

Cutadapt

Download Link :- NA

Installation :-

Open Terminal and type the following command :-

(OR)

R-base

R-base

R-base

Download Link :- NA

Installation :-

Open Terminal and type the following command :-

R-studio

R-studio

R-studio

Download Link :- https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb

Installation :-

Open Terminal and type the following command :-

If the command is giving Error

RNA Seq (Reference Based)

RNA Seq (Reference Based)

1 : Samtools

install the required packages :-

Download Link :-

Download Link of samtools :-

Make Install

Add the installed path to the bash.bashrc file

2 : BWA

Download Link :- https://sourceforge.net/projects/bio-bwa/files/latest/download?source=typ_redirect

download, extract them and Add the path in the "/etc/bash.bashrc file"

(OR)

For Installation via terminal :-

Open Terminal and type the following command :-

3 : Tophat2

Download Link :- http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz

download, extract them and Add the path in the "/etc/bash.bashrc file"

(OR)

For Installation via termianal :-

Open Terminal and type the following command :-

4 : Bowtie

Download Link :- https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip/download

download, extract them and Add the path in the "/etc/bash.bashrc file"

(OR)

For Installation via termianal :-

Open Terminal and type the following command :-

5 : cufflinks

Download Link :- http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz

download, extract them and Add the path in the "/etc/bash.bashrc file"

6 : IGV

Download Link :- http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.13.zip

download, extract them and Add the path in the "/etc/bash.bashrc file"

RNA Seq (De-novo Based)

RNA Seq (De-novo Based)

1 : Trinity

Install the required packages :-

Download Link :-

download, extract them and Add the path in the "/etc/bash.bashrc file"

Installation

download, extract them and Add the path in the "/etc/bash.bashrc file"

Installation :-

2 : Transdecoder

Download Link :- https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.3.0.tar.gz

Installation :-

Extract TransDecoder-v5.3.0.tar.gz

Download, extract them and Add the path in the "/etc/bash.bashrc file" run with :-

3 : BLAST

Installation :-

Open Terminal and type the below command

Download Link :-
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip

Download Link :-
NA

Download Link :-
NA

Download Link :-
https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb

Download Link :-
https://sourceforge.net/projects/bio-bwa/files/latest/download?source=typ_redirect

Download Link :-
http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz

Download Link :-
https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip/download

Download Link :-
http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz

Download Link :-
http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.13.zip

Download Link :-
https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.3.0.tar.gz

Download Link :-
https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip/download

Download Link :-
NA

Download Link :-
https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb

Download Link :-
https://sourceforge.net/projects/snpeff/files/latest/download?source=files

Download Link :-
https://sourceforge.net/projects/bio-bwa/files/latest/download?source=typ_redirect

Download Link :-
http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.13.zip

Download Link :-
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip

Download Link :-
https://github.com/FelixKrueger/Bismark/archive/master.zip

Bismark requires

Bowtie2 or Bowtie1

Samtools

Download Link :-
NA

Download Link :-
https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb

Download Link :-
https://github.com/rajewsky-lab/mirdeep2/archive/master.zip