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

igdtools

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

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.

umierrorcorrect2

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

exomeflow

Production-quality Whole Exome Sequencing analysis pipeline

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

ilus

ilus: A handy tools for generating WGS/WES analysis pipeline.

tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

arvia

ARVIA: Antibiotic Resistance Variant Identifier for Pseudomonas aeruginosa

biokevlar

Reference-free variant discovery in large eukaryotic genomes

pepper-polish

PEPPER-Margin-DeepVariant

diffbio

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

basevar

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

snipgenie

variant calling and phylogenies from microbial WGS data

rmetl

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