Workshop • Intro to Bioinformatics using NGS data • 5 days

This repository contains an analysis pipeline developed to characterize WGS output

Nextflow Tutorial - Variant Calling Edition

Automated end to end NGS exome analysis pipeline. One command from FASTQ to fully annotated variants with QC, alignment, GATK calling, ANNOVAR and snpEff annotation, functional classification, and final ZIP packaging.

NextFlow pipeline for Virus Variant calling and de novo Assembly of Nanopore and Illumina Reads

Shell workflow designed to process Whole Exome Sequencing (WES) data following GATK4 best practices for variant calling.

SNP calling pipeline for clonal Ascochyta rabiei

A fully automated and reproducible Whole Genome Sequencing (WGS) pipeline built with Snakemake. Implements GATK Best Practices for alignment (BWA), variant calling, and functional annotation (SnpEff) on human (GRCh38) data.

Repository detailing a Nextflow pipeline to run mpileup variant callling on TF footprints.

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

A Tufts University Research Technology Workshop

This repository provides a comprehensive module on graphical pangenomics, guiding users through building, indexing, mapping, and visualizing pangenome graphs. The module runs on Google Cloud Platform using Jupyter notebooks and includes tools like PGGB, vg, BLAST, and Bandage.

github website

Bioinformatics analysis pipeline to call SNPs from Papaya genotypes for population genetics and GWAS analyses

End-to-end NGS variant calling and functional annotation pipeline for Limulus polyphemus using GATK and SnpEff, with biological interpretation of high-impact immune and metabolic variants.

Genomic Analysis Pipeline: Automate data preprocessing, variant calling, and annotation with Snakemake. Ensure reproducibility and reliability in genomic studies.