GitHub topics: variant-calling
thom-99/benchmarking_vcallers
benchmarking variant callers for ONT long reads (in banana) - EI summer project
Language: Jupyter Notebook - Size: 817 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0
ANSES-Ploufragan/vvv2_display
Create png file of variants proportions in an assembly/reference including CDS positions using output of vadr 1.5.1 (annotation) and vardict-java 1.8.3 (variant calling)
Language: Python - Size: 4.37 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 1 - Forks: 0
PacificBiosciences/sawfish
Joint structural variant and copy number variant caller for HiFi sequencing data
Language: Rust - Size: 1.16 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 60 - Forks: 4
TileDB-Inc/TileDB-VCF
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Language: C++ - Size: 34.9 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 97 - Forks: 17
nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Language: Nextflow - Size: 107 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 473 - Forks: 472
ShujiaHuang/BaseVar2
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: 4.58 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 0
nf-core/rnavar
gatk4 RNA variant calling pipeline
Language: Nextflow - Size: 4.29 MB - Last synced at: 2 days ago - Pushed at: 10 days ago - Stars: 53 - Forks: 41
nf-core/variantbenchmarking
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
Language: Nextflow - Size: 21.7 MB - Last synced at: 2 days ago - Pushed at: 5 days ago - Stars: 35 - Forks: 16
ghga-de/nf-platypusindelcalling
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
Language: Python - Size: 119 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 2 - Forks: 0
nf-core/raredisease
Call and score variants from WGS/WES of rare disease patients.
Language: Nextflow - Size: 188 MB - Last synced at: 3 days ago - Pushed at: 18 days ago - Stars: 108 - Forks: 49
tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
Language: Python - Size: 18.2 MB - Last synced at: 2 days ago - Pushed at: 14 days ago - Stars: 850 - Forks: 195
Janespercy/somatic-variant-ml-pipeline
Machine learning pipeline for predicting pathogenicity of somatic variants in cancer genomics using Snakemake and scikit-learn
Language: Python - Size: 31.3 KB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0
HKU-BAL/ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
Language: Python - Size: 12.1 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 68 - Forks: 4
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
Language: Nextflow - Size: 10.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 141 - Forks: 133
nf-core/pacvar
Longread PacBio sequencing processing for WGS and PureTarget
Language: Nextflow - Size: 345 MB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 11 - Forks: 8
pdimens/harpy
Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!
Language: Python - Size: 471 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 18 - Forks: 2
pablo-aja-macaya/ARVIA
ARVIA: Antibiotic Resistance Variant Identifier for Pseudomonas aeruginosa
Language: Python - Size: 9.77 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 0
cidgoh/nf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.
Language: Python - Size: 76.7 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 9 - Forks: 5
NBISweden/workshop-ngsintro
Workshop • Intro to Bioinformatics using NGS data • 5 days
Language: HTML - Size: 499 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 15 - Forks: 7
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: 855 KB - Last synced at: 5 days ago - Pushed at: 4 months ago - Stars: 139 - Forks: 35
allytrope/variant-analysis
A Snakemake pipeline for variant calling of genomic FASTQ data using GATK
Language: Jupyter Notebook - Size: 4.46 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 5 - Forks: 0
AMRmicrobiology/WGS-Analysis-VariantCalling
Nextflow pipeline for whole-genome sequencing (WGS) analysis and variant calling in bacterial genomes using Illumina data, supporting de novo assembly and reference-based analysis.
Language: Nextflow - Size: 937 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 3 - Forks: 0
genomicssport/varlinker
exact point variant annotation
Language: Rust - Size: 124 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0
bbglab/deepUMIcaller
A Nextflow pipeline for duplex sequencing data analysis
Language: Nextflow - Size: 152 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 1
EUCANCan/variant-callers
Scripts and containers to run the variant callers originally used in ONCOLINER
Language: Shell - Size: 247 MB - Last synced at: about 18 hours ago - Pushed at: 12 months ago - Stars: 3 - Forks: 0
EUCANCan/variant-extractor
Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.
Language: Python - Size: 6.5 MB - Last synced at: about 18 hours ago - Pushed at: 5 months ago - Stars: 7 - Forks: 1
gmboowa/rMAP-2.0
This tool provides a modular WDL-Docker-Cromwell environment for rMAP, a bioinformatics pipeline for analyzing microbial genomic data, genome assembly & profiling of the resistome, mobilome & virulome, as well as pangenome & MLST typing, BLASTn & phylogenetic analysis. It includes all required tools, enabling reproducible & scalable analysis
Language: WDL - Size: 28 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 1 - Forks: 0
flalom/vcf-reformatter
🧬 High-performance VCF file parser and reformatter with VEP annotation support. Converts complex VCF files to analyzable TSV format with intelligent transcript handling.
Language: Rust - Size: 112 KB - Last synced at: 1 day ago - Pushed at: 23 days ago - Stars: 36 - Forks: 3
gear-genomics/tracy
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
Language: C++ - Size: 2.97 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 114 - Forks: 21
suhrig/arriba
Fast and accurate gene fusion detection from RNA-Seq data
Language: C++ - Size: 24.2 MB - Last synced at: 16 days ago - Pushed at: 17 days ago - Stars: 245 - Forks: 54
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: 100 MB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 106 - Forks: 24
tseemann/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Language: Perl - Size: 124 MB - Last synced at: about 22 hours ago - Pushed at: about 1 year ago - Stars: 542 - Forks: 116
IdoBar/SNP_Calling_Papaya
Bioinformatics analysis pipeline to call SNPs from Papaya genotypes for population genetics and GWAS analyses
Language: HTML - Size: 1.12 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0
aprilweilab/pyigd
Python-only parser for Indexable Genotype Data (IGD) format.
Language: Python - Size: 52.7 KB - Last synced at: about 20 hours ago - Pushed at: 2 months ago - Stars: 6 - Forks: 0
oicr-gsi/strelkaSomatic
Strelka2 somatic variant calling workflow
Language: WDL - Size: 62.5 KB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 1 - Forks: 0
NVIDIA/VariantWorks
Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/
Language: Python - Size: 10.1 MB - Last synced at: 9 days ago - Pushed at: 18 days ago - Stars: 46 - Forks: 12
fullscreen-triangle/gospel
Python framework for comprehensive variant detection in whole genome sequences using advanced machine learning models for cross domain pattern recognition in fitness, pharmacogenetics and nutritional aspects of sprint running
Language: Makefile - Size: 60 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 1 - Forks: 0
oicr-gsi/hmmcopy
Calls Copy Number Variants on sequencing data from cancer patients
Language: WDL - Size: 56.6 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 3 - Forks: 1
genomic-medicine-sweden/nallo
An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
Language: Nextflow - Size: 101 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 33 - Forks: 11
ShujiaHuang/mitoquest
Human Mitochondrial sequencing data Analysis Toolkit. Fetching information like variants, heteroplasmy/homoplasmy, etc. on mitochondrial genome from sequencing data
Language: C - Size: 27.7 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 4 - Forks: 0
IdoBar/HPC_SNP_calling_documentation
SNP calling pipeline for clonal Ascochyta rabiei
Language: HTML - Size: 73.8 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0
annmariyaes/chipcallvar
chipcallvar is a reproducible Nextflow workflow to call somatic variants (SNVs and INDELs) on ChIP-seq data primarily taking advantage of macs3 callvar, GATK mutect2 and freebayes variant callers.
Language: Nextflow - Size: 4.31 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - 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: 7.41 MB - Last synced at: 2 days ago - Pushed at: 20 days ago - Stars: 9 - Forks: 0
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: 16.8 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 125 - Forks: 42
gear-genomics/indigo
Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
Language: JavaScript - Size: 1.14 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 36 - Forks: 9
kishwarshafin/pepper
PEPPER-Margin-DeepVariant
Language: Python - Size: 36.1 MB - Last synced at: 17 days ago - Pushed at: over 1 year ago - Stars: 253 - Forks: 42
lh3/fermikit
De novo assembly based variant calling pipeline for Illumina short reads
Language: TeX - Size: 7.45 MB - Last synced at: 7 days ago - Pushed at: almost 5 years ago - Stars: 108 - Forks: 21
MPUSP/snakemake-simple-mapping
A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.
Language: Python - Size: 2.48 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0
Clinical-Genomics/BALSAMIC
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Language: Python - Size: 229 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 49 - Forks: 15
kcleal/dysgu
Toolkit for calling structural variants using short or long reads
Language: Cython - Size: 46.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 107 - Forks: 13
HKU-BAL/Clair3
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Language: Python - Size: 3.97 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 292 - Forks: 32
sdegeorgia/CANVAS-summary
CNV Analysis Next-gen Variant Assessment Suite
Size: 2.93 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
broadinstitute/long-read-pipelines
Long read production pipelines
Language: Jupyter Notebook - Size: 220 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 147 - Forks: 25
sequana/sequana
Sequana: a set of Snakemake NGS pipelines
Language: Jupyter Notebook - Size: 35.7 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 146 - 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: 19 days ago - Pushed at: about 1 month ago - Stars: 27 - Forks: 8
tylergross97/pdx_somatic_variant_calling
A containerized bioinformatics pipeline built with Nextflow to identify somatic (acquired) mutations in the tumor of patient-derived xenograft (PDX) models, a common analysis performed in preclinical and oncology research labs
Language: Nextflow - Size: 161 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 0
macyEpell/Pell_GBS_Genomics
This repository contains scripts used to collect and analyze data from whole genome sequences of clinical Streptococcus agalactiae (Group B Strep) isolates for the project described in the following manuscript: Pell, M.E. et al., bioRxiv, 2024-04-01.
Language: R - Size: 46.9 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
BioJulia/SequenceVariation.jl
Biological sequence variation
Language: Julia - Size: 371 KB - Last synced at: 13 days ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 3
LeoooJR/DIVV
Differential Investigation of Variability in Variants
Language: C - Size: 7.31 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0
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.
Language: Python - Size: 24.9 MB - Last synced at: 4 days ago - Pushed at: over 2 years ago - Stars: 204 - Forks: 27
atks/vt
A tool set for short variant discovery in genetic sequence data.
Language: C - Size: 30.1 MB - Last synced at: 6 days ago - Pushed at: over 4 years ago - Stars: 200 - Forks: 3
BiodataAnalysisGroup/synth4bench Fork of sfragkoul/synth4bench
A framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.
Language: R - Size: 242 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 1
sfragkoul/synth4bench
A framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.
Language: R - Size: 242 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 2
TimD1/vcfdist
vcfdist: Accurately benchmarking phased variant calls
Language: C++ - Size: 85.3 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 81 - Forks: 8
vcflib/vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Language: C++ - Size: 34 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 649 - Forks: 224
sanger-tol/variantcalling
Nextflow DSL2 pipeline to call variants on long read alignment.
Language: Nextflow - Size: 3.91 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 8 - Forks: 9
Illumina/paragraph
Graph realignment tools for structural variants
Language: C++ - Size: 30.8 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 158 - Forks: 28
Sydney-Informatics-Hub/Bioinformatics
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.
Size: 178 KB - Last synced at: 22 days ago - Pushed at: 2 months ago - Stars: 17 - Forks: 1
CTrierMaansson/DNAfusion
Identification of gene-fusions, including EML4-ALK
Language: R - Size: 63.2 MB - Last synced at: 9 days ago - Pushed at: 4 months ago - Stars: 4 - Forks: 1
karajones/capture
Plethodontid salamander DNA capture kit
Language: Shell - Size: 3.83 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
luntergroup/octopus
Bayesian haplotype-based mutation calling
Language: C++ - Size: 138 MB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 312 - Forks: 37
aprilweilab/picovcf
Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.
Language: C++ - Size: 568 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 17 - Forks: 0
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: 3 months ago - Pushed at: over 6 years ago - Stars: 87 - 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: 3 days ago - Pushed at: over 2 years ago - Stars: 61 - Forks: 9
NIGMS/Intro-to-Pangenomics
This repository provides a comprehensive module on graphical pangenomics, guiding users through building, indexing, mapping, and visualizing pangenome graphs. The module runs on Google Cloud Platform using Jupyter notebooks and includes tools like PGGB, vg, BLAST, and Bandage.
Language: HTML - Size: 22.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
YanshengLuo/singlecell-variantcalling-pipeline
This repository provides an end-to-end workflow for variant calling from single-cell RNA-seq data (scRNA-seq) using Cell Ranger, custom Python BAM splitting, and cellsnp-lite. The pipeline works with 10x Genomics and Drop-seq data and supports human and mouse genomes.
Language: Shell - Size: 15.6 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
aleponce4/hantavirus-pipeline
Bioinformatics pipeline for processing Hantavirus NGS data with a two-pass approach. Implements quality control, reference-based mapping, metaconsensus refinement, variant calling, and automatic negative sample detection. Features include primer evaluation, coverage visualization, and comparison between consensus sequences.
Language: Python - Size: 124 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
oicr-gsi/delly
Delly workflow produces a set of vcf files with different types of structural variant calls
Language: WDL - Size: 356 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 1 - Forks: 2
oicr-gsi/varscan
varscan repo contains code for Varscan workflow
Language: WDL - Size: 124 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
IBCHgenomic/webanno
a unified platform for variant search
Language: TypeScript - Size: 31.3 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
mbhall88/NanoVarBench
Evaluating Nanopore-based bacterial variant calling
Language: Python - Size: 39.1 MB - Last synced at: 8 days ago - Pushed at: about 2 months ago - Stars: 19 - Forks: 1
gmboowa/ASFV-ONT-Gen
ASFV-ONT-Gen is a pipeline for analyzing African Swine Fever Virus (ASFV) whole-genome sequencing data generated using Oxford Nanopore Technology (ONT). It supports genome assembly, variant calling & phylogenetic analysis, enabling rapid genomic insights for surveillance & outbreak investigation
Language: Python - Size: 1.89 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
ValldHebron-Bioinformatics/minMutFinder
Tool written in Python and Bash implemented in a Nextflow pipeline that accurately identifies mutations and assesses their frequencies, accounting for multiple nucleotide mutations occurring within a single codon. Additionally, it can annotate mutations associated to phenotypical changes in viral populations based on user-supplied datasets.
Language: Python - Size: 79.7 MB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0
gmboowa/nf-rMAP
nf-rMAP: Nextflow-powered microbial genomics pipeline for rapid antimicrobial resistance analysis. Implements rMAP's core functionality with cloud-native scalability, enhanced QC, & modular workflows. Processes Illumina data through assembly, annotation, AMR detection & phylogenetics.
Language: Nextflow - Size: 1.27 MB - Last synced at: 25 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
gmboowa/GenoSweep
GenoSweep is an automated genomic analysis pipeline processing raw FASTQs through quality control, host read removal, reference alignment (BWA), variant calling (bcftools), and consensus generation. Designed for pathogen/viral genomes, it ensures efficient, standardized processing from raw reads
Language: Shell - Size: 9.77 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
LilValero/Human-Exome-Variant-calling-Using-Illumina-Data
Bioinformatics pipeline for Illumina human exome variant calling using FastQC, Trimmomatic, BWA, Samtools, Bcftools, and SnpEff. Demonstrates a reproducible workflow for NGS data analysis. #bioinformatics #genomics #variant-calling #ngs #pipeline
Language: HTML - Size: 638 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
BCCDC-PHL/alignment-variants
Pipeline to perform alignment & variant calling on whole-genome sequence data
Language: Python - Size: 3.18 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0
mcvickerlab/varCA
Use an ensemble of variant callers to call variants from ATAC-seq data
Language: Python - Size: 357 KB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 23 - Forks: 7
dmnfarrell/snipgenie
command line and desktop tool for microbial variant calling
Language: Jupyter Notebook - Size: 134 MB - Last synced at: 21 days ago - Pushed at: 4 months ago - Stars: 9 - Forks: 0
pblaney/mgp1000
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
Language: Nextflow - Size: 324 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 11 - Forks: 5
jahetzler/jahetzler.github.io
github website
Language: HTML - Size: 15 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
lh3/minipileup
Simple pileup-based variant caller
Language: C - Size: 120 KB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 89 - Forks: 9
oicr-gsi/freec
freec workflow - call CNV on your tumor wih optional normal
Language: WDL - Size: 87.9 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
tobiasrausch/nRex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
Language: Shell - Size: 1.87 MB - Last synced at: 2 days ago - Pushed at: 5 months ago - Stars: 12 - Forks: 2
meeranhussain/Population_genomic_analysis
A repository for efficient population genomic analysis using Snakemake workflow.
Language: R - Size: 919 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
CRG-CNAG/CalliNGS-NF
GATK RNA-Seq Variant Calling in Nextflow
Language: Nextflow - Size: 29 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 133 - Forks: 53
kehrlab/PopDel
Population-wide Deletion Calling
Language: C++ - Size: 20.5 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 35 - Forks: 2
ratope/VariantFilteringCriteriaVvTempranillo
List of the filtering criteria of the variants called in samples of Vitis vinifera cv. Tempranillo
Size: 85.9 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
HKU-BAL/Clair3-RNA
Clair3-RNA - a long-read small variant caller for RNA sequencing data
Language: Python - Size: 528 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 22 - Forks: 1
GiuseppeBocci/Pipeline-for-Biallelic-Rare-Genetic-Disorders
Genomics 2025/2026 Project a bit enhanced :)
Language: Shell - Size: 12.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
