Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

✂️ Trim sequencing adapters from NGS data automatically

This repository contains the code pipeline I developed for Next Generation Sequencing (NGS) analysis during my internship at CSIR-IGIB, New Delhi. The project was completed under the guidance of Mr. Sunil Nagpal and Dr. Bhupesh Taneja. For detailed instructions and a better understanding of pipeline, please refer to the README.md file.

Dockerized cutadapt

Metabarcoding analysis pipeline, using DADA2 and qiime2

Script to unzip, clean, assemble, and convert illumina pair-end fastq files in all subdirectories for 16S amplicon data (V3, V4 and V3-V4 regions).

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.