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Variant Calling Python Packages

Python packages with the GitHub topic variant-calling. Sorted by relevance, with stars and monthly downloads.
kcleal
dysgu

Toolkit for calling structural variants using short or long reads

5K 115 14
sequana
sequana

Sequana: a set of Snakemake NGS pipelines

3K 151 27
tanghaibao
jcvi

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

2K 909 199
imrobintomar
exomeflow

Production-quality Whole Exome Sequencing analysis pipeline

2K 0 0
avitai
diffbio

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

1K 1 0
ShujiaHuang
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.

866 143 36
aprilweilab
igdtools

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

616 22 0
nanoporetech
megalodon

Nanopore base calling augmentation.

559 204 27
czbiohub
cerebra

finds mutants in your scRNA-seq experiment

509 62 9
sfilges
umierrorcorrect2

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

451 0 0
mbhall88
tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

378 14 2
EUCANCan
variant-extractor

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

361 7 1
dib-lab
biokevlar

Reference-free variant discovery in large eukaryotic genomes

310 42 9
kishwarshafin
pepper-polish

PEPPER-Margin-DeepVariant

284 258 42
pablo-aja-macaya
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.

181 1 0
ShujiaHuang
basevar

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

144 28 8
dmnfarrell
snipgenie

command line and desktop tool for microbial variant calling

83 10 0
tjiangHIT
rmetl

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

35 21 4
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