variant-calling | Topic | Ecosyste.ms: Repos

Topic: "variant-calling"

tanghaibao/jcvi

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

Language: Python - Size: 18.8 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 812 - Forks: 190

vcflib/vcflib

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

Language: C++ - Size: 33.3 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 642 - Forks: 223

tseemann/snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

Language: Perl - Size: 124 MB - Last synced at: 1 day ago - Pushed at: 9 months ago - Stars: 508 - Forks: 118

nf-core/sarek

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

Language: Nextflow - Size: 100 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 439 - Forks: 439

luntergroup/octopus

Bayesian haplotype-based mutation calling

Language: C++ - Size: 137 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 304 - Forks: 38

HKU-BAL/Clair3

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

Language: Python - Size: 3.35 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 273 - Forks: 31

kishwarshafin/pepper

PEPPER-Margin-DeepVariant

Language: Python - Size: 36.1 MB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 247 - Forks: 42

suhrig/arriba

Fast and accurate gene fusion detection from RNA-Seq data

Language: C++ - Size: 24.1 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 235 - Forks: 52

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.

Language: Python - Size: 24.9 MB - Last synced at: 17 days ago - Pushed at: almost 2 years ago - Stars: 200 - Forks: 27

atks/vt

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

Language: C - Size: 30.1 MB - Last synced at: 14 minutes ago - Pushed at: almost 4 years ago - Stars: 196 - Forks: 3

broadinstitute/viral-ngs

Viral genomics analysis pipelines

Language: Python - Size: 64.5 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 192 - Forks: 68

aquaskyline/Clairvoyante

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

Language: Python - Size: 894 MB - Last synced at: 10 days ago - Pushed at: over 1 year ago - Stars: 169 - Forks: 27

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced at: 13 days ago - Pushed at: over 2 years ago - Stars: 156 - Forks: 28

sequana/sequana

Sequana: a set of Snakemake NGS pipelines

Language: Jupyter Notebook - Size: 35.8 MB - Last synced at: about 15 hours ago - Pushed at: about 2 months ago - Stars: 146 - Forks: 27

broadinstitute/long-read-pipelines

Long read production pipelines

Language: Jupyter Notebook - Size: 220 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 145 - Forks: 25

tseemann/nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

Language: Perl - Size: 11.3 MB - Last synced at: 11 days ago - Pushed at: about 1 year ago - Stars: 139 - Forks: 38

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.

Language: Python - Size: 845 KB - Last synced at: 10 days ago - Pushed at: 4 months ago - Stars: 132 - Forks: 35

CRG-CNAG/CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

Language: Nextflow - Size: 29 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 129 - Forks: 52

nf-core/viralrecon

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

Language: Nextflow - Size: 9.84 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 121 - Forks: 108

andersen-lab/ivar Fork of gkarthik/ivar

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

Language: C++ - Size: 16.3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 120 - Forks: 42

PacificBiosciences/ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Size: 34.1 MB - Last synced at: 9 months ago - Pushed at: about 1 year ago - Stars: 113 - Forks: 31

mcveanlab/mccortex

De novo genome assembly and multisample variant calling

Language: C - Size: 9.86 MB - Last synced at: 5 months ago - Pushed at: about 6 years ago - Stars: 113 - Forks: 25

lh3/fermikit

De novo assembly based variant calling pipeline for Illumina short reads

Language: TeX - Size: 7.45 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 108 - Forks: 22

gear-genomics/tracy

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Language: C++ - Size: 4.73 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 107 - Forks: 21

kcleal/dysgu

Toolkit for calling structural variants using short or long reads

Language: Cython - Size: 46.4 MB - Last synced at: about 7 hours ago - Pushed at: about 8 hours ago - Stars: 102 - Forks: 13

HKU-BAL/Clair

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

Language: Python - Size: 1.01 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 102 - Forks: 12

nf-core/raredisease

Call and score variants from WGS/WES of rare disease patients.

Language: Nextflow - Size: 186 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 98 - Forks: 44

moiexpositoalonsolab/grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

Language: Python - Size: 99.9 MB - Last synced at: 11 days ago - Pushed at: 26 days ago - Stars: 96 - Forks: 22

iqbal-lab-org/gramtools

Genome inference from a population reference graph

Language: C++ - Size: 14.7 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 95 - Forks: 15

GenomicsDB/GenomicsDB

High performance data storage for importing, querying and transforming variants.

Language: C++ - Size: 66 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 94 - Forks: 18

TileDB-Inc/TileDB-VCF

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Language: C++ - Size: 34.7 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 93 - Forks: 16

humanlongevity/HLA

xHLA: Fast and accurate HLA typing from short read sequence data

Language: Jupyter Notebook - Size: 91.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 92 - Forks: 51

lh3/minipileup

Simple pileup-based variant caller

Language: C - Size: 116 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 88 - Forks: 6

bioinformatics-centre/BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers

Language: C++ - Size: 1.75 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 83 - Forks: 8

TimD1/vcfdist

vcfdist: Accurately benchmarking phased variant calls

Language: C++ - Size: 85.8 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 80 - Forks: 7

czbiohub-sf/cerebra 📦

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

Language: Python - Size: 164 MB - Last synced at: about 16 hours ago - Pushed at: over 2 years ago - Stars: 60 - Forks: 9

HKU-BAL/ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Language: Python - Size: 9.89 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 59 - Forks: 4

lh3/CHM-eval

Language: TeX - Size: 524 KB - Last synced at: about 1 month ago - Pushed at: almost 5 years ago - Stars: 53 - Forks: 8

PacificBiosciences/sawfish

Structural variant discovery and genotyping from mapped PacBio HiFi data

Language: Rust - Size: 693 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 48 - Forks: 2

karel-brinda/ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

Language: C++ - Size: 3.49 MB - Last synced at: 16 days ago - Pushed at: over 6 years ago - Stars: 47 - Forks: 3

Clinical-Genomics/BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Language: Python - Size: 229 MB - Last synced at: about 13 hours ago - Pushed at: about 14 hours ago - Stars: 46 - Forks: 16

nf-core/rnavar

gatk4 RNA variant calling pipeline

Language: Nextflow - Size: 4.2 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 46 - Forks: 37

NVIDIA/VariantWorks

Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/

Language: Python - Size: 10.1 MB - Last synced at: 17 days ago - Pushed at: over 2 years ago - Stars: 45 - Forks: 11

gencorefacility/variant-calling-pipeline-gatk4

Variant Calling Pipeline Using GATK4 and Nextflow

Language: Nextflow - Size: 23.4 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 40 - Forks: 40

kevlar-dev/kevlar

Reference-free variant discovery in large eukaryotic genomes

Language: Python - Size: 71.5 MB - Last synced at: 9 months ago - Pushed at: almost 4 years ago - Stars: 40 - Forks: 9

nf-core/deepvariant Fork of lifebit-ai/DeepVariant 📦

Please consider using/contributing to https://github.com/nf-core/sarek

Language: Nextflow - Size: 7.18 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 40 - Forks: 18

brentp/indelope

find large indels (in the blind spot between GATK/freebayes and SV callers)

Language: Nim - Size: 133 KB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 39 - Forks: 1

kehrlab/PopDel

Population-wide Deletion Calling

Language: C++ - Size: 20.5 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 35 - Forks: 2

gear-genomics/indigo

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Language: JavaScript - Size: 3.04 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 31 - Forks: 7

oliverSI/GATK4_Best_Practice

GATK4 Best Practice Nextflow Pipeline

Size: 9.77 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 29 - Forks: 28

ShujiaHuang/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

Language: C - Size: 46.2 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 27 - Forks: 7

genomic-medicine-sweden/nallo

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Language: Nextflow - Size: 98.1 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 26 - Forks: 8

SUwonglab/arcsv

Complex structural variant detection from WGS data

Language: Python - Size: 5.11 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 26 - Forks: 8

sib-swiss/NGS-variants-training

GitHub for the SIB courses NGS - Genome variant analysis

Language: Shell - Size: 69.4 MB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 25 - Forks: 9

aryarm/varCA

Use an ensemble of variant callers to call variants from ATAC-seq data

Language: Python - Size: 349 KB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 23 - Forks: 7

HKU-BAL/Clair3-RNA

Clair3-RNA - a long-read small variant caller for RNA sequencing data

Language: Python - Size: 528 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 22 - Forks: 1

IKIM-Essen/uncovar

Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.

Language: Python - Size: 3.83 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 20 - Forks: 4

Sentieon/sentieon-dnaseq 📦

Sentieon DNAseq

Language: Shell - Size: 60.5 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 19 - Forks: 12

sanjaynagi/rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Language: Jupyter Notebook - Size: 99.5 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 18 - Forks: 9

mbhall88/NanoVarBench

Evaluating Nanopore-based bacterial variant calling

Language: Python - Size: 37.4 MB - Last synced at: 5 days ago - Pushed at: 4 months ago - Stars: 18 - Forks: 1

tjiangHIT/rMETL

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

Language: Python - Size: 1.02 MB - Last synced at: 8 days ago - Pushed at: 8 months ago - Stars: 18 - Forks: 4

Sydney-Informatics-Hub/Bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

Size: 173 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 1

pdimens/harpy

Process haplotagging data, from raw sequences to phased haplotypes, batteries included.

Language: Python - Size: 466 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 16 - Forks: 2

adrianodemarino/Imputation_beagle_tutorial

Imputation-beagle-tutorial

Size: 12.7 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 16 - Forks: 2

NBISweden/workshop-ngsintro

Workshop • Intro to Bioinformatics using NGS data • 5 days

Language: HTML - Size: 497 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 14 - Forks: 7

nf-core/vipr 📦

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

Language: Nextflow - Size: 217 KB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 14 - Forks: 10

nf-core/exoseq 📦

Please consider using/contributing to https://github.com/nf-core/sarek

Language: Nextflow - Size: 2.77 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 14 - Forks: 25

nshomron/hoobari

Bayesian-based fetal genotyping using maternal cell-free DNA and parental sequencing data.

Language: Python - Size: 16.4 MB - Last synced at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 13 - Forks: 3

tobiasrausch/nRex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

Language: Shell - Size: 1.87 MB - Last synced at: 9 days ago - Pushed at: 13 days ago - Stars: 12 - Forks: 2

Sentieon/sentieon-dnascope-ml

Sentieon DNAscope + Machine Learning Model

Language: Shell - Size: 111 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 4

HKU-BAL/Clair3-Trio

Clair3-Trio: variant calling in trio using Nanopore long-reads

Language: Python - Size: 2.74 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 12 - Forks: 1

TimD1/nPoRe

nPoRe: n-Polymer Realigner for improved pileup-based variant calling

Language: Python - Size: 493 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 12 - Forks: 0

collaborativebioinformatics/Sniphles

Sniphles is a read-based phasing approach for phased variant calling of structural variants.

Language: Python - Size: 2.44 MB - Last synced at: 3 months ago - Pushed at: over 4 years ago - Stars: 12 - Forks: 2

yjx1217/Varathon

A scalable variant calling and benchmarking framework supporting both short and long reads.

Language: Perl - Size: 1.03 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 11 - Forks: 4

nf-core/variantbenchmarking

A nextflow variant benchmarking pipeline - premature

Language: Nextflow - Size: 3.66 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 11 - Forks: 7

fedarko/strainFlye

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes

Language: Python - Size: 14.4 MB - Last synced at: 21 days ago - Pushed at: 7 months ago - Stars: 11 - Forks: 2

mbhall88/tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

Language: Python - Size: 3.32 MB - Last synced at: 5 days ago - Pushed at: 10 months ago - Stars: 11 - Forks: 2

CMU-SAFARI/Genome-on-Diet

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

Language: Roff - Size: 63 MB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 4

koesterlab/microphaser

Language: Rust - Size: 1.91 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 2

VCCRI/dv-trio

dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.

Language: Shell - Size: 165 KB - Last synced at: 12 days ago - Pushed at: about 4 years ago - Stars: 11 - Forks: 1

KChen-lab/MonoVar

Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data

Language: Python - Size: 13.5 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 11 - Forks: 6

pblaney/mgp1000

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

Language: Nextflow - Size: 324 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 10 - Forks: 4

abs-tudelft/variant-calling-at-scale

Scalable and High Performance Variant Calling on Cluster Environments

Language: Python - Size: 818 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 0

INMEGEN/Pipelines_Inmegen

Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica para el procesamiento de datos genómicos y transcriptómicos.

Language: Nextflow - Size: 7.37 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 9 - Forks: 0

DKFZ-ODCF/SNVCallingWorkflow

The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow

Language: Python - Size: 738 KB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 9 - Forks: 4

nf-core/pacvar

Longread PacBio sequencing processing for WGS and PureTarget

Language: Nextflow - Size: 345 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 6

bpucker/NAVIP

Neighborhood-Aware Variant Impact Predictor

Language: Python - Size: 328 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 1

dmnfarrell/snipgenie

command line and desktop tool for microbial variant calling

Language: Jupyter Notebook - Size: 133 MB - Last synced at: about 17 hours ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 0

kaist-ina/RUN-DVC

Generalizing deep learning-based variant callers via domain adaptation and semi-supervised learning

Language: Python - Size: 3.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0

BioJulia/SequenceVariation.jl

Biological sequence variation

Language: Julia - Size: 371 KB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 3

CMU-SAFARI/Molecules2Variations

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957

Size: 4.31 MB - Last synced at: 9 months ago - Pushed at: almost 3 years ago - Stars: 8 - Forks: 0