A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

Docker container for W2RAP based on CentOS

This repository contains my end-of-degree project. I've implemented a simple version of three of the most known aligners like Bowtie, BWA and BWT-SM

Wrapper scripts for TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) and UNEAK (Universal Network Enabled Analysis Kit) v3.0 Genotyping by Sequencing (GBS) analysis pipelines and GBS statistics generation

The second part of https://github.com/npanuhin/BIOCAD

The snakyVC pipeline is designed for efficiently and parallelly executing variant calling on next-generation sequencing (NGS) whole-genome datasets.

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Tech Stack: React, and Tailwind CSS

Dockerized BWA (Burrow-Wheeler Aligner for short-read alignment)

Server-Side BWA MERN 2021

Bioinformatics pipeline for Illumina human exome variant calling using FastQC, Trimmomatic, BWA, Samtools, Bcftools, and SnpEff. Demonstrates a reproducible workflow for NGS data analysis. #bioinformatics #genomics #variant-calling #ngs #pipeline

This is a shell-scripted bioinformatics pipeline to process NGS data into interpretable mutation and somatic variant calls and finally visualising them in IGV. It integrates industry-standard tools and supports automated execution.

Build Docker container for BWA and (optionally) convert to Apptainer/Singularity.

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Complete pipeline that mirrors the manuscript: reference based assembly with depth masking, de novo checks, phylogeny with configurable models including ModelFinder, and targeted mutation analysis for G and F versus NC_038235.1 and NC_001781.1. Includes CI and environment files for easy setup.

Backend StayCation

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Germline variant calling pipeline