Whole Genome Sequencing Python Packages

gambit

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

ore

Associate outliers with rare variation

pynnotator

This is a Genome Annotation Framework developed with the goal of annotating VCF files (Exomes or Genomes) from patients with Mendelian Disorders.

doublehelix

Genomic data manipulation tool

lionheart

LIONHEART detects cancer from whole genome sequenced plasma cell-free DNA.

cfdnalab

Ultra-fast command line tools for extracting bias-corrected fragmentation patterns from cell-free DNA

gnomad-db

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

ilus

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.

mitywgs

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

handygenome

An interacitve python interface for inspection of somatic mutations

arvia

ARVIA: Antibiotic Resistance Variant Identifier for Pseudomonas aeruginosa

vsnpdev

vSNP -- validate SNPs