NGS Analysis Pipeline

Installation of Tools

Before running the data analysis pipeline, we need to install the following tools:

1. fastqc: A quality control tool for high-throughput sequence data.

   • Mac: Install using Homebrew - brew install fastqc

2. trimmomatic: A tool for trimming and filtering raw sequencing data.

   • Download from: Trimmomatic Website

3. hisat2: A fast and sensitive alignment program for mapping next-generation sequencing reads to a reference genome.

   • Download from: Hisat2 Website

4. sra toolkit: A suite of tools for accessing and working with data in the Sequence Read Archive (SRA).

   • Install according to instructions from: SRA Toolkit GitHub

5. sam toolkit: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format

   • Download from: Sam Toolkit

Prepare Data

To use the data analysis pipeline, follow these steps to download and prepare the data:

1. Go to the NCBI SRA website: NCBI SRA and find the datasets of interest.

2. Download the data in SRA format. For example, if the accession number is SRR23683396, you can download it using the following command in the directory where you want to store the data:

   prefetch SRR23683396
   
   fastq_dump  SRR23683396.sra
   
   
   

Running Pipeline:

Finally, adjust the variable names and the commands in the script, and run

./scripts/pipeplie.sh