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GUI/CommandLine Tool Box for biologistists to utilize NGS data.

A complete begineers guide to learn shell scripting from scratch which includes Videos, Practice scenarios and project idea.

The Secure Microsoft Windows Downloader

🐳📊📚 Docker Images tracking the stable Galaxy releases.

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

DNA sequencing analysis notes from Ming Tang

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

Making whole bacterial genome sequencing data analysis easy

MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.

Bioinformatics analysis scripts, workflows, general code examples

VAPiD: Viral Annotation and Identification Pipeline

Variant Interpretation Pipeline

MAG Circularization Method

This repository contains course materials from JAX-BD2K workshop.

Automated next generation DNA sequencing analysis pipeline suited for clinical tests, with >99.9% sensitivity to Sanger sequencing at read-depth>18

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

Introme prioritises coding and noncoding splice-altering variants for clinical variant interpretation

This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.

NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC

Mostly useful scripts and files for processing MiSeq amplicon data

Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.

Collection of notes and scripts related to NGS

NIPT-human-genetics is a semi-automated workflow designed for the analysis of large-scale ultra-low-pass non-invasive prenatal test (NIPT) sequencing data in human genetic studies.

A reliable gap filling pipeline for draft genomes

A pipeline on WES(whole exome sequence) analysis, from data download to analysis

A methodological framework to conduct a calibrated gene-based rare variant association test by leveraging the genome aggregation database (gnomAD) as an external control dataset

Functional code templates for the Star Protocols paper describing consolidated WES variant calling with 3 callers

Automated Pipeline for Variant/Haplotype Calling and Filtering