Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary

Whole Exome/Whole Genome Sequencing alignment pipeline

Clinical Whole Genome and Exome Sequencing Pipeline

Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.

An R package for summarizing and visualizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies generated by STAARpipeline

Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

🐳 Dockerized WES pipeline for variants identification in mathced tumor-normal samples

Constructing Neoantigen Vaccine Pipeline with pVACtools

LOVD+ -- LOVD for diagnostics: analysis of whole-exome data using LOVD.

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

An app for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline in UK Biobank RAP

Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.

WDL-based pipelines

An app for automatically functionally annotating the variants of whole-genome/whole-exome sequencing (WGS/WES) studies and integrating the functional annotations with the genotype data using FAVORannotator in UK Biobank RAP

A lightweight R package for performing association meta-analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using MetaSTAARlite pipeline

Workflows for whole-genome/exome sequencing data analysis