Bioinformatics Procedure for NGS Data Analysis
A step-by-step Bioinformatics procedure for Next-Generation Sequencing (NGS) are, Data quality control using tools like FastQC to assess raw data. Data preprocessing for adapter trimming and low-quality base removal with tools like Trimmomatic or FastP. Read mapping to a reference genome using aligners such as BWA or Bowtie2. Post-alignment processing including duplicate removal with Picard and variant calling with GATK or Samtools. Downstream analysis and visualization for specific applications like differential gene expression or variant interpretation using tools like R packages or IGV. A more detailed breakdown of those were given below 1. Data Quality Control (QC) Purpose: To check the quality of the raw sequencing reads and identify any potential issues. Tools: FastQC: A widely used tool to generate quality control reports for raw sequencing data. Output: A report summarizing metrics like Phred scores, adapter contamination, and sequence q...