PacificBiosciences/sawfish

Structural variant discovery and genotyping from mapped PacBio HiFi data

Language: Rust - Size: 693 KB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 48 - Forks: 2

DanielRivasMD/genomic_structures

Library for interacting with genomic structures, namely mobile elements and structural variants.

Language: Rust - Size: 242 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 0

kehrlab/PopDel

Population-wide Deletion Calling

Language: C++ - Size: 20.5 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 35 - Forks: 2

PacificBiosciences/SVTopo

Complex structural variant visualization for HiFi sequencing data

Language: HTML - Size: 115 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 26 - Forks: 2

senzhaocode/FuSViz

A web-browser app to visualise, interpret and prioritise genomic/transcriptomic structural variations (SVs) of multiple samples.

Language: JavaScript - Size: 86.8 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 10 - Forks: 4

AmpliconSuite/ecSimulator

Simulate ecDNA structures with user-specified properties.

Language: Python - Size: 57.5 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 3

ACEnglish/truvari

Structural variant toolkit for VCFs

Language: Python - Size: 151 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 351 - Forks: 50

barricklab/seabreeze Fork of ira-zibbu/seabreeze-ltee-analysis

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies

Language: Python - Size: 19.9 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 1

ACEnglish/kanpig

Kmer Analysis of Pileups for Genotyping

Language: Rust - Size: 5.01 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 27 - Forks: 1

broadinstitute/gatk-sv

A structural variation pipeline for short-read sequencing

Language: Python - Size: 84.6 MB - Last synced at: 8 days ago - Pushed at: 10 days ago - Stars: 187 - Forks: 75

tobiasrausch/nRex

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

Language: Shell - Size: 1.87 MB - Last synced at: 7 days ago - Pushed at: 11 days ago - Stars: 12 - Forks: 2

Illumina/manta 📦

Structural variant and indel caller for mapped sequencing data

Language: C++ - Size: 113 MB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 423 - Forks: 152

oicr-gsi/delly

Delly workflow produces a set of vcf files with different types of structural variant calls

Language: WDL - Size: 339 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1 - Forks: 2

tjiangHIT/cuteSV

Long read based human genomic structural variation detection with cuteSV

Language: Python - Size: 3.12 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 258 - Forks: 37

guillaume-gricourt/HmnFusion

A tool to aggregate results of fusion produced by Genefuse and Lumpy and calculate allelic frequency

Language: HTML - Size: 6.06 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0

tprodanov/locityper

Targeted genotyper for complex polymorphic genes

Language: Rust - Size: 1.58 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 20 - Forks: 0

tobiasrausch/vc

A tutorial on structural variant calling for short read sequencing data

Language: R - Size: 111 KB - Last synced at: 7 days ago - Pushed at: 6 months ago - Stars: 32 - Forks: 2

SAMtoBAM/MUMandCo

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation

Language: Shell - Size: 4.59 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 66 - Forks: 15

oicr-gsi/mavis

MAVIS workflow, annotation of structural variants

Language: WDL - Size: 110 KB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 0 - Forks: 1

sbslee/pypgx

A Python package for pharmacogenomics (PGx) research

Language: Python - Size: 224 MB - Last synced at: 11 days ago - Pushed at: 2 months ago - Stars: 70 - Forks: 17

fritzsedlazeck/Sniffles

Structural variation caller using third generation sequencing

Language: Python - Size: 12.4 MB - Last synced at: 9 days ago - Pushed at: 27 days ago - Stars: 584 - Forks: 96

hall-lab/svtools

Tools for processing and analyzing structural variants.

Language: Python - Size: 154 MB - Last synced at: 15 days ago - Pushed at: almost 3 years ago - Stars: 151 - Forks: 55

tobiasrausch/sv

Structural variant calling tutorial using long-reads.

Language: R - Size: 55.7 KB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 4 - Forks: 0

bcgsc/mavis

Merging, Annotation, Validation, and Illustration of Structural variants

Language: Python - Size: 20.8 MB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 75 - Forks: 14

XiaoTaoWang/NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

Language: Python - Size: 59.8 MB - Last synced at: 27 days ago - Pushed at: over 1 year ago - Stars: 63 - Forks: 16

suhrig/arriba

Fast and accurate gene fusion detection from RNA-Seq data

Language: C++ - Size: 24.1 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 235 - Forks: 52

SandraLouise/SVJedi-graph

SV genotyper for long reads with a variation graph

Language: Python - Size: 11.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 0

iprada/Circle-Map

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

Language: Python - Size: 3.75 MB - Last synced at: 8 days ago - Pushed at: 9 months ago - Stars: 62 - Forks: 19

Han-Cao/HarmoniSV

A toolkit to harmonize and filter structural variations across methods and samples.

Language: Python - Size: 5.23 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

Han-Cao/collapse-bubble

Merge structural variations (SV) for pangenome VCF

Language: Python - Size: 156 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 4 - Forks: 0

brentp/smoove

structural variant calling and genotyping with existing tools, but, smoothly.

Language: Go - Size: 2.49 MB - Last synced at: 9 days ago - Pushed at: 10 months ago - Stars: 248 - Forks: 21

kcleal/SV_Benchmark_CMRG_GIAB

Structural variant benchmark

Language: Nextflow - Size: 435 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 1

MeHelmy/princess

Language: Python - Size: 1.51 MB - Last synced at: 13 days ago - Pushed at: about 2 months ago - Stars: 79 - Forks: 8

dellytools/delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Language: C++ - Size: 37.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 458 - Forks: 139

dellytools/sansa

Structural variant VCF annotation, duplicate removal and comparison

Language: C++ - Size: 203 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 29 - Forks: 1

Illumina/witty.er

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

Language: C# - Size: 110 MB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 32 - Forks: 1

edawson/svaha2

Linear-time, low-memory construction of variation graphs

Language: C++ - Size: 609 KB - Last synced at: 18 days ago - Pushed at: about 5 years ago - Stars: 20 - Forks: 0

brentp/duphold

don't get DUP'ed or DEL'ed by your putative SVs.

Language: Nim - Size: 8.16 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 104 - Forks: 9

dzyim/List-of-Structural-Variation-Detection-Software

Size: 5.86 KB - Last synced at: 5 days ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1

DanielRivasMD/Chapulin

Caught on the jump! Next-generation genomic mobile element and structural variant identification tool.

Language: Rust - Size: 1.25 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

laura-budurlean/Structural_Variant_Discovery

A combination of optical genome mapping with Bionano and whole genome sequencing short-read data. This pipeline was created to help integrate structural variant calling from these two technologies.

Language: Shell - Size: 15.9 MB - Last synced at: 30 days ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

fritzsedlazeck/SVCollector

Method to optimally select samples for validation and resequencing

Language: C++ - Size: 1.98 MB - Last synced at: 11 days ago - Pushed at: about 4 years ago - Stars: 27 - Forks: 5

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced at: 11 days ago - Pushed at: over 2 years ago - Stars: 156 - Forks: 28

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

murphycj/AGFusion

Python package to annotate and visualize gene fusions.

Language: Python - Size: 345 MB - Last synced at: 9 days ago - Pushed at: 7 months ago - Stars: 61 - Forks: 26

hall-lab/sv-pipeline

Pipeline for structural variation detection in cohorts

Language: wdl - Size: 941 KB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 49 - Forks: 20

senzhaocode/FuSViz_docs

Documentation of FuSViz app

Size: 28.6 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

mehrdadbakhtiari/adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

Language: Python - Size: 1.42 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 41 - Forks: 15

rhshah/iCallSV

A Framework to call Structural Variants from NGS based datasets

Language: Python - Size: 3.12 MB - Last synced at: 17 days ago - Pushed at: about 7 years ago - Stars: 22 - Forks: 10

nanoporetech/pipeline-structural-variation 📦

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Language: Python - Size: 6.22 MB - Last synced at: 15 days ago - Pushed at: over 3 years ago - Stars: 114 - Forks: 17

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

DKFZ-ODCF/ACEseqWorkflow

Allele-specific copy number estimation with whole genome sequencing

Language: R - Size: 15.5 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 10

nf-cmgg/structural

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

Language: Nextflow - Size: 5.37 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 19 - Forks: 2

Oshlack/MINTIE

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

Language: Python - Size: 21.8 MB - Last synced at: 5 months ago - Pushed at: 10 months ago - Stars: 34 - Forks: 7

rhshah/iAnnotateSV

iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Generation DNA sequencing data.

Language: Python - Size: 23.1 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 16 - Forks: 11

laura-budurlean/SV-calling-with-SpeedSeq

A workflow for using SpeedSeq to align and call SVs from WGS data

Language: Shell - Size: 15.6 KB - Last synced at: 30 days ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

yjx1217/simuG

simuG: a general-purpose genome simulator

Language: Perl - Size: 5.17 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 83 - Forks: 11

beroukhim-lab/SVsig

Language: MATLAB - Size: 16.5 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1

alok123t/HyINDEL

Hybrid approach for detection of Insertions and Deletions from NGS data

Language: C++ - Size: 4.6 MB - Last synced at: 3 months ago - Pushed at: about 5 years ago - Stars: 5 - Forks: 0

ITBE-Lab/MA

The Modular Aligner and The Modular SV Caller

Language: C++ - Size: 11.4 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 46 - Forks: 3

kcleal/dysgu

Toolkit for calling structural variants using short or long reads

Language: Cython - Size: 46.3 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 85 - Forks: 10

complexgenome/CUMC_taub

Language: R - Size: 374 KB - Last synced at: 10 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

vpc-ccg/svict

Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA

Language: C++ - Size: 280 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 24 - Forks: 6

samanthaleejensen/svfindermanual

Guide to installing, using, and interpreting structural variant finders. Includes example scripts for running tools on UCLA's Hoffman2 and a description of how to use the machine learning combination method FusorSV.

Language: Shell - Size: 12.7 KB - Last synced at: 11 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

cgroza/GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

Language: R - Size: 39.2 MB - Last synced at: 11 months ago - Pushed at: 12 months ago - Stars: 79 - Forks: 3

mattravenhall/SV-Pop

Upscaling SV detection to a multi-population level.

Language: Python - Size: 455 KB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 21 - Forks: 1

shaze/h3acnvcalls

Supporting material for H3Africa Structural and Copy Number Variant paper: summary data and scripts

Language: Nextflow - Size: 6.25 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

CarolinaPB/population-structural-var-calling-smoove

population structural variant calling with smoove

Language: Python - Size: 1.84 MB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 3

Chenglin20170390/Haplotype-diversity

This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato breeding“

Language: Python - Size: 101 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 3

bio-ontology-research-group/DeepSVP

Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity

Language: Python - Size: 843 KB - Last synced at: about 23 hours ago - Pushed at: about 3 years ago - Stars: 16 - Forks: 4

LorenaDerezanin/Tayra_Genome_Project

De novo genome assembly, phylogenetics, comparative genomics analysis, and functional variant annotation

Language: Shell - Size: 10.5 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

akcorut/kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Language: Python - Size: 610 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 24 - Forks: 5

dantaki/SV2

Support Vector Structural Variation Genotyper

Language: Python - Size: 10.3 MB - Last synced at: 9 months ago - Pushed at: almost 5 years ago - Stars: 58 - Forks: 11

KCCG/ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

Language: Perl - Size: 961 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 61 - Forks: 7

galantelab/sandy

A straightforward and complete next-generation sequencing read simulator

Language: Perl - Size: 25.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 15 - Forks: 2

asylvz/CONGA

CONGA: COpy Number Genotyping in Ancient genomes and low-coverage sequencing data

Language: C - Size: 1.38 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 0

pengsl-lab/SVPath

An accurate pipeline for predicting the pathogenicity of human exon structural variants

Language: Perl - Size: 10.5 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 3

jeongdo801/scNOVA

scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis

Language: R - Size: 56.6 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 3

vpc-ccg/sedef

Identification of segmental duplications in the genome

Language: C++ - Size: 20.7 MB - Last synced at: 6 months ago - Pushed at: about 3 years ago - Stars: 26 - Forks: 8

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

bourgeron-lab/gollum

detection of rings on acrocentric chromosomes using short reads sequencing

Language: Python - Size: 2.48 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

collaborativebioinformatics/SVTeaser

SV simulation for rapid benchmarking

Language: Jupyter Notebook - Size: 6.1 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 2

biowdl/germline-DNA

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

Language: wdl - Size: 8.93 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 22 - Forks: 7

c-braeunig/structural-variation-viewer

A suite of Python-based command line tools to visualize structural variation

Language: Python - Size: 4.54 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

nriddiford/svParser

Explore and filter structural variant calls from Lumpy and Delly VCF files

Language: Perl - Size: 4.07 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 8 - Forks: 1

nriddiford/svSupport

A tool to find reads supporting/opposing structural variant breakpoints

Language: Python - Size: 2.57 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1

nriddiford/svBreaks

Analysis and plotting functions for structural variant breakpoint data

Language: R - Size: 7.84 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

nriddiford/svMech

Predict mechanism underlying structural variants

Language: Python - Size: 2.02 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

morispi/LEVIATHAN

Linked-reads based structural variant caller with barcode indexing

Language: C++ - Size: 49.9 MB - Last synced at: 9 months ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 2

redndgreen8/hmcnc

Hidden Markov Model based Copy number caller

Language: Python - Size: 28.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 1

zlye/RVE

Code used to discover structural variants, SNP, Indels that were applied to rare variant analysis

Language: Python - Size: 45.9 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

weigelworld/minitv

Alignment frontend for AliTV

Language: Python - Size: 146 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 2

fabio-cunial/pav-wdl Fork of broadinstitute/pav-wdl

Runs several variant callers that align an assembly to a reference

Language: wdl - Size: 9.12 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

sigven/sv_anno

Processing and annotation of somatic structural variants

Language: Python - Size: 1.95 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

RajLabMSSM/snakeSV

Snakemake pipeline for SV discovery and analysis

Language: Python - Size: 401 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

ACEnglish/TruvariData

Data and Scripts relevant to the development and benchmarking of truvari

Language: Jupyter Notebook - Size: 27.6 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

Kingsford-Group/squid

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Language: C++ - Size: 17.5 MB - Last synced at: 7 months ago - Pushed at: about 3 years ago - Stars: 40 - Forks: 22

smehringer/SViper

Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

Language: C++ - Size: 6.65 MB - Last synced at: 17 days ago - Pushed at: over 2 years ago - Stars: 32 - Forks: 8

FunGeST/Palimpsest

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

Language: R - Size: 58.2 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 67 - Forks: 19

katarinastuart/Sv5_StarlingWGS

Scripts and notes related to the manuscript: Stuart KC, Edwards, RJ, Sherwin WB, Rollins, LA. 2022 Contrasting patterns of single nucleotide polymorphisms and structural variations across multiple invasions. Molecular Biology and Evolution, 40(3): msad046. https://doi.org/10.1093/molbev/msad046

Size: 949 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0