Variant Calling Python Packages

contig

An agentic bioinformatics analyst: it runs the analysis on your own compute, self-heals failures, verifies the output, and returns a reproducible result.

dysgu

Toolkit for calling structural variants using short or long reads

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

igdtools

Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.

sequana

Sequana: a set of Snakemake NGS pipelines

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

octopusv

Merge and compare structural variants across callers, samples, and platforms. Standardizes BND-heavy output from GRIDSS, SvABA, Sniffles, and more.

megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

variant-extractor

Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.

cerebra

A tool for fast and accurate summarizing of variant calling format (VCF) files

tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

umierrorcorrect2

Pipeline for UMI error correction and variant calling from amplicon sequencing data

cbicall

CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis-ready VCFs across heterogeneous computing environments.

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.

pepper-polish

PEPPER-Margin-DeepVariant

biokevlar

Reference-free variant discovery in large eukaryotic genomes

arvia

ARVIA: Antibiotic Resistance Variant Identifier for Pseudomonas aeruginosa

basevar

This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT data

snipgenie

command line and desktop tool for microbial variant calling

rmetl

rMETL - realignment-based Mobile Element insertion detection Tool for Long read