Bioinformatics Tools

Author: Puspendu Sardar, Ph.D., Deprtment of Medicine, University of Cambridge

This repository contains scripts for basic bioinformatics analyses and utilities.

Tools Included

1. sequence_stats.sh: Bash script to calculate sequence statistics from a FASTA file.

   • Usage: bash sequence_stats.sh <input.fasta>

2. nucleotide_frequency.R: R script to generate a nucleotide frequency bar plot.

   • Usage: Rscript nucleotide_frequency.R <input.fasta>

3. fastq_stats.py: Calculates basic statistics for FASTQ files.

   • Usage: python fastq_stats.py <input.fastq>

4. alpha_diversity.R: Calculates different diversity indices from species count data.

   • Usage: Rscript alpha_diversity.R <count_data.tab> <diversity_results.txt>

5. DADA2.R: Runs DADA2 on paired-end amplicon sequencing reads.

   • Usage: Rscript DADA2.R

Requirements

• Python
• R-package seqinr
• R-package DADA2

How to Clone and Run

git clone https://github.com/yourusername/bioinformatics-tools.git
cd bioinformatics-tools