Whole Genome Sequencing Python Packages

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.

lionheart

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

doublehelix

Genomic data manipulation tool

ore

Associate outliers with rare variation

gnomad-db

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

mitywgs

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

vsnpdev

vSNP -- validate SNPs

handygenome

An interacitve python interface for inspection of somatic mutations

arvia

ARVIA (Antibiotic Resistance Variant Identifier for Pseudomonas aeruginosa) takes single-end/paired-end reads and/or assemblies to perform exhaustive variant calling of genes related to antibiotic resistance in Pseudomonas aeruginosa.