Variant Calling Python Packages

dysgu

Toolkit for calling structural variants using short or long reads

sequana

Sequana: a set of Snakemake NGS pipelines

jcvi

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

exomeflow

Production-quality Whole Exome Sequencing analysis pipeline

diffbio

End-to-end differentiable bioinformatics pipelines built on JAX/Flax NNX

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.

igdtools

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

megalodon

Nanopore base calling augmentation.

cerebra

finds mutants in your scRNA-seq experiment

umierrorcorrect2

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

tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

variant-extractor

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

biokevlar

Reference-free variant discovery in large eukaryotic genomes

pepper-polish

PEPPER-Margin-DeepVariant

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.

basevar

BaseVar: A python software for calling variants from ultra low pass WGS data.

snipgenie

command line and desktop tool for microbial variant calling

rmetl

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