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

Whole Genome Sequencing analysis, WGS analysis

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

An R package for performing STAAR procedure in whole-genome sequencing studies

vcfdist: Accurately benchmarking phased variant calls

Detect novel (and reference) STR expansions from short-read data

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

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

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

A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.

Clinical Whole Genome and Exome Sequencing Pipeline

Whole Exome/Whole Genome Sequencing alignment pipeline

Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.

An R package for performing MetaSTAAR procedure in whole-genome sequencing studies

JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes