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.

A bioinformatics pipeline for variant calling and benchmarking using DeepVariant and Clair3, evaluated against the GIAB HG002 truth set.

Nextflow DSL2 pipeline for PacBio HiFi variant calling. Supports minimap2 and pbmm2 alignment with bcftools, Clair3, and DeepVariant variant callers. Fully containerized with Docker. Packaged with benchmarking tools for method validation and testing.

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

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.

SNP calling pipeline for clonal Ascochyta rabiei

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

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 comprehensive NGS analysis pipeline for E. coli (K-12): Includes QC with FastQC, alignment using Bowtie2, and variant calling for genomic research.

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

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.