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variant-calling

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tanghaibao /jcvi

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

bioinformatics genomics assembly blast comparative-genomics variant-calling synteny sequence-alignments genome-sequencing genetic-maps allmaps

UpdatedFeb 15, 2026
Python

vcflib /vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

genomics variant-calling genotyping haplotypecaller vcf-manipulation

UpdatedOct 31, 2025
C++

tseemann /snippy

✂️ ⚡ Rapid haploid variant calling and core genome alignment

bioinformatics snps genomics vcf variant-calling bacteria indel-discovery haploid fastq-analysis

UpdatedDec 12, 2025
Perl

nf-core /sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

workflow bioinformatics pipeline annotation genomics nextflow cancer reproducible-research containers conda next-generation-sequencing variant-calling somatic germline whole-exome-sequencing whole-genome-sequencing pre-processing nf-core gatk4 target-panels

UpdatedFeb 20, 2026
Nextflow

HKU-BAL /Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

deep-learning nanopore genomics computational-biology pacbio variant-calling illumina long-reads variant-detection ont-data ont-models

UpdatedFeb 18, 2026
Python

luntergroup /octopus

Bayesian haplotype-based mutation calling

bioinformatics genomics somatic-variants haplotypes variants variant-calling single-cell phasing de-novo-mutation

UpdatedFeb 13, 2026
C++

suhrig /arriba

Fast and accurate gene fusion detection from RNA-Seq data

rna-seq cancer gene-fusion star variant-calling virus-integration structural-variation fusion-genes gene-fusions fusion-gene

UpdatedSep 21, 2025
C++

kishwarshafin /pepper

PEPPER-Margin-DeepVariant

nanopore variants variant-calling oxford-nanopore genome-variation long-reads pacbio-ccs assembly-polishing

UpdatedJan 12, 2024
Python

atks /vt

A tool set for short variant discovery in genetic sequence data.

variant-calling

UpdatedMay 4, 2021
C

nanoporetech /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.

epigenetics variant-calling basecalling guppy

UpdatedMay 4, 2023
Python

broadinstitute /viral-ngs

viral-ngs: command line tools and wrappers for processing raw viral genomic data

python docker bioinformatics genomics genome ngs variant-calling bam genome-sequencing illumina fastq genome-assembly variant-annotations viral-ngs viral

UpdatedFeb 17, 2026
Python

aquaskyline /Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

bioinformatics deep-learning computational-biology variant-calling

UpdatedDec 26, 2023
Python

Illumina /paragraph

Graph realignment tools for structural variants

vcf variant-calling htslib structural-variation genotyping

UpdatedDec 8, 2022
C++

nf-core /viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

workflow nanopore virus pipeline nextflow assembly metagenomics variant-calling illumina oxford-nanopore amplicon viral ont nf-core long-read-sequencing artic covid-19 covid19 sars-cov-2

UpdatedJan 22, 2026
Nextflow

sequana /sequana

Sequana: a set of Snakemake NGS pipelines

coverage rna-seq snakemake taxonomy ngs pacbio variant-calling de-novo sequanix

UpdatedJan 22, 2026
Jupyter Notebook

broadinstitute /long-read-pipelines

Long read production pipelines

pipelines wdl variant-calling de-novo-assembly long-reads

UpdatedFeb 20, 2026
Jupyter Notebook

tseemann /nullarbor

💾 📃 "Reads to report" for public health and clinical microbiology

public-health report variant-calling bacteria fastq phylogenomics denovo-assembly genotyping resistome virulome

UpdatedDec 9, 2025
Perl

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.

bioinformatics pipeline bioinformatics-pipeline variant-calling workflow-management whole-genome-sequencing

UpdatedMay 20, 2025
Python

CRG-CNAG /CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

bioinformatics rna-seq genomics nextflow ngs gatk variant-calling

UpdatedDec 14, 2022
Nextflow

ivar

andersen-lab /ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

variant-calling amplicon-sequencing

UpdatedFeb 16, 2026
C++

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