Installation of required softwares

1) FastQC

Find the appropriate version comaptible for your operating system from here

$ wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
$ unzip fastqc_v0.12.1.zip

2) Trimmomatic

$ wget https://github.com/usadellab/Trimmomatic/files/5854859/Trimmomatic-0.39.zip
$ unzip Trimmomatic-0.39.zip

3) Burrows-Wheeler Aligner

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

4) Samtools and htslib suit

You don’t hae to get the htslib separately.

$ wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2
$ tar -xvzf samtools-1.18.tar.bz2 && cd samtools-1.18
$ ./configure --prefix=/your/soft/path/name/
$ make
$ make install
$ export PATH="/your/soft/path/name/samtools-1.18/bin:$PATH"

5) Picard Tools

$ git clone https://github.com/broadinstitute/picard.git
$ cd picard
$ ./gradlew shadowJar

6) Bioawk

$ sudo git clone https://github.com/lh3/bioawk.git
$ cd bioawk/
$ sudo make
$ ./bioawk

7) BCFTools

$ wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2
$ tar -xjvf bcftools-1.10.2.tar.bz2
$ cd bcftools-1.10.2
$ make
$ sudo make prefix=/usr/local/bin install
$ sudo ln -s /usr/local/bin/bin/bcftools /usr/bin/bcftools # you don't technically need to do this. And if you aren't a root user you may get a ``permission denied`` message - don't worry about it.

8) PSMC

$ git clone https://github.com/lh3/psmc.git
$ cd psmc
$ make
$ cd utils
$ make

9) R and R-Studio

Download R first - For Machttps://cran.r-project.org/bin/macosx/

For Windows : https://cran.r-project.org/bin/windows/base/

Now Download R-Studio. R-Studio is an IDE which helps you access R interactively. Alternatively you can use any other IDE like VS Code. Download the R-Studio - https://posit.co/download/rstudio-desktop/