Installing Anaconda [ Why do we need it? ]

Check other lighter and faster versions: Miniconda, Miniforge, Mamba & Minimamba

1. Navigate to Desktop

   $ cd Desktop

2. Make a directory 'bgap' and a sub-directory 'resources' & navigate to it

   $ mkdir bgap
                 $ mkdir bgap/resources
                 $ cd bgap/resources

3. Download Anaconda script

   $ wget https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh

4. Change permissions and install

   $ chmod +x Anaconda3-2022.10-Linux-x86_64.sh
               $ Anaconda3-2022.10-Linux-x86_64.sh

5. Follow onscreen instructions. Install in the default directory. On restarting the Terminal, (base) prefix will be shown. Check the installed environments

   $ conda info --envs

6. Add Bioconda channel

   $ conda config --add channels defaults
               $ conda config --add channels bioconda
               $ conda config --add channels conda-forge
               $ conda config --set channel_priority strict

7. Update conda (optional step)

   $ conda update -n base -c defaults conda

Installing sra-tools

1. Create a new environment sra

   $ conda create -n sra -y

2. Deactivate base environment and activate sra environment

   $ conda deactivate
                 $ conda activate sra

3. Install the latest version of sra-tools from anaconda.org

   $ conda install -c bioconda sra-tools=3.0

4. Check the installation

   $ srapath --version

Downloading a dataset of raw reads from NCBI SRA

1. While in the resources directory, download Helicobacter pylori raw reads. Check description of the dataset.

   $ prefetch SRR22388518 -p

   If downloaded successfully, the following message will appear

   2023-03-09T14:56:10 prefetch.3.0.3: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
               2023-03-09T14:56:11 prefetch.3.0.3: 1) Downloading 'SRR22388518'...
               2023-03-09T14:56:11 prefetch.3.0.3: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
               2023-03-09T14:56:11 prefetch.3.0.3:  Downloading via HTTPS...
               |-------------------------------------------------- 100%   
               2023-03-09T15:13:42 prefetch.3.0.3:  HTTPS download succeed
               2023-03-09T15:13:43 prefetch.3.0.3:  'SRR22388518' is valid
               2023-03-09T15:13:43 prefetch.3.0.3: 1) 'SRR22388518' was downloaded successfully
               2023-03-09T15:13:43 prefetch.3.0.3: 'SRR22388518' has 0 unresolved dependencies

2. Convert to FASTQ files and delete the downloaded directory

   $ fasterq-dump SRR22388518/SRR22388518.sra
                 $ rm -r SRR22388518

3. Move FASTQ files to a new directory and rename.

   $ mkdir ../reads
               $ mv *fastq ../reads/
               $ cd ../reads
               $ mv SRR22388518_1.fastq a45_R1.fastq 
               $ mv SRR22388518_2.fastq a45_R2.fastq

4. We now have the required raw reads

Installing QC packages

1. Deactivate sra environment and create qc environment

   $ conda deactivate
               $ conda create -n qc -y
             

2. Activate qc and install FastQC, BBDuk and Trimmomatic(Optional) - Always check the versions

   $ conda activate qc
                 $ conda install -c bioconda fastqc trimmomatic bbmap

3. Check installations

   $ fastqc
               $ trimmomatic -version
               $ bbduk.sh -h

Installing Mapping Tools

1. Deactivate qc environment and create mappers environment

   $ conda deactivate
               $ conda create -n mappers -y
             

2. Activate mappers and install bwa, bcftools, and samtools

   $ conda activate mappers
                 $ conda install -c bioconda bwa bcftools samtools

3. Check installations

   $ bwa
               $ bcftools -h
               $ samtools --help
             

4. Probable Error samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory
   Fedora users:

   $ sudo dnf install ncurses-libs
               $ sudo dnf install ncurses-devel
               $ sudo dnf install ncurses-compat-libs
             

   Ubuntu users:

   $ sudo apt-get install libncurses5
               $ sudo apt-get install ia32-libs
             

5. Install bam2fastq. It requires an older version of samtools. Create new environment

   $ conda deactivate
               $ conda create -n bam2fastq -y
               $ conda activate bam2fastq
               $ conda install -c yuxiang bam2fastq

6. Install emboss in a new environment

   $ conda deactivate
               $ conda create -n emboss -y
               $ conda activate emboss
               $ conda install -c bioconda emboss
             

Download Reference Genome from NCBI for Mapping
Helicobacter pylori A45

Installing Assembling Tools

1. Deactivate mappers environment and create assemblers environment

   $ conda deactivate
               $ conda create -n assemblers -y
             

2. Activate assemblers. Install SPAdes & Barrnap

   $ conda activate assemblers
               $ conda install -c bioconda spades barrnap

3. Check installations

   $ spades -h
               $ barrnap --help