Simple NGS Analysis Pipeline

Processing NGS data has never been that easy.

Simple NGS Analysis Pipeline

This pipeline is designed to process Next-Generation Sequencing (NGS) data, perform quality control, trim the reads, align them to a reference genome, and call variants using common bioinformatics tools.

NGS Analysis Pipeline

Pipeline Overview

  • Data Download (wget): Downloads the paired-end reads & the reference genome files in the precised directory.
  • Quality Control (FastQC): Assess the quality of raw reads.
  • Trimming (FastP): Trim low-quality bases and adapters from the reads.
  • Genome Mapping (BWA): Align the trimmed reads to the reference genome.
  • Variant Calling (FreeBayes): Identify variants (SNPs and indels) from the aligned reads.

Requirements

For this pipeline, you will need the following tools:

  • fastqc
  • fastp
  • bwa
  • samtools
  • bcftools
  • freebayes

Install them with setup.sh:

bash setup.sh

Running the Pipeline

The pipeline can be executed by running the script.sh file. The script downloads the data then processes them before performing the full NGS analysis.

bash script.sh

After running the pipeline, you will get the following files of interest:

  • The downloaded data
    • Forward reads: ERR8774458_1.fastq.gz
    • Reverse reads: ERR8774458_2.fastq.gz
    • Reference genome: Reference.fasta
  • The output
    • out_R1.fq.gz, out_R2.fq.gz: Trimmed paired-end reads
    • out.bam: Aligned reads in BAM format
    • var.vcf: Variant call format (VCF) file with identified variants

More dataset to try the pipeline on

Reference

https://raw.githubusercontent.com/josoga2/yt-dataset/main/dataset/raw_reads/reference.fasta

ACBarrie

Alsen

Baxter

Chara

Drysdale