sra-toolkit

A demo workflow showing download, extraction, and compression of sequences from SRA.

fast utils for fetch and dump NCBI SRA archive raw data

Reproducible NGS data analysis pipeline for SRA datasets, covering raw-read QC, adapter and quality trimming, post-trimming QC, MultiQC reporting, read alignment, BAM processing, and downstream analysis.

This repository contains an end-to-end tumour-only somatic variant-calling pipeline (GATK Mutect2 + snpEff) for triple-negative breast cancer whole-exome data, focused on BRCA1/BRCA2/TP53, built on Google Colab via Visual Studio Code.

High Throughput Sequencing at your fingertips

Whole Genome Sequencing (WGS) analysis pipeline for Bacillus subtilis using Linux and Bioinformatics tools.

Repository for bulk RNA-seq analyses (from undergrad 2nd-3rd year) – Reorganized

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.

Contract-driven HPC pipeline for deterministic SRA data acquisition from NCBI BioProjects, featuring strict preflight validation, reproducible tool environments, and SLURM-native execution.

Proof of concept of a SRA to trimmed FASTQ (including quality control) pipeline with Nextflow

A contract-driven, SLURM-native HPC pipeline for deterministic conversion of SRA archives to FASTQ, featuring strict preflight validation, reproducible tool installation, and restart-safe, per-sample execution.

Automated environmental DNA (eDNA) metabarcoding pipeline for converting NCBI SRA sequencing data into taxonomically annotated species tables.