Topic: "structural-variation"
fritzsedlazeck/Sniffles
Structural variation caller using third generation sequencing
Language: Python - Size: 12.4 MB - Last synced at: 15 days ago - Pushed at: about 1 month ago - Stars: 584 - Forks: 96
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
Illumina/manta 📦
Structural variant and indel caller for mapped sequencing data
Language: C++ - Size: 113 MB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 423 - Forks: 152
ACEnglish/truvari
Structural variant toolkit for VCFs
Language: Python - Size: 151 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 354 - Forks: 51
tjiangHIT/cuteSV
Long read based human genomic structural variation detection with cuteSV
Language: Python - Size: 3.12 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 258 - Forks: 37
brentp/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
Language: Go - Size: 2.49 MB - Last synced at: 16 days ago - Pushed at: 10 months ago - Stars: 248 - Forks: 21
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
broadinstitute/gatk-sv
A structural variation pipeline for short-read sequencing
Language: Python - Size: 84.6 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 187 - Forks: 75
Illumina/paragraph
Graph realignment tools for structural variants
Language: C++ - Size: 30.8 MB - Last synced at: 17 days ago - Pushed at: over 2 years ago - Stars: 156 - Forks: 28
hall-lab/svtools
Tools for processing and analyzing structural variants.
Language: Python - Size: 154 MB - Last synced at: 21 days ago - Pushed at: almost 3 years ago - Stars: 151 - Forks: 55
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: 21 days ago - Pushed at: over 3 years ago - Stars: 114 - Forks: 17
brentp/duphold
don't get DUP'ed or DEL'ed by your putative SVs.
Language: Nim - Size: 8.16 MB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 104 - Forks: 9
kcleal/dysgu
Toolkit for calling structural variants using short or long reads
Language: Cython - Size: 46.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 102 - Forks: 13
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
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
MeHelmy/princess
Language: Python - Size: 1.51 MB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 79 - Forks: 8
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: 12 months ago - Pushed at: 12 months ago - Stars: 79 - Forks: 3
bcgsc/mavis
Merging, Annotation, Validation, and Illustration of Structural variants
Language: Python - Size: 20.8 MB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 75 - Forks: 14
sbslee/pypgx
A Python package for pharmacogenomics (PGx) research
Language: Python - Size: 224 MB - Last synced at: 17 days ago - Pushed at: 2 months ago - Stars: 70 - Forks: 17
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
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: 28 days ago - Pushed at: 28 days ago - Stars: 66 - Forks: 15
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: 2 days ago - Pushed at: over 1 year ago - Stars: 64 - Forks: 16
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: 15 days ago - Pushed at: 9 months ago - Stars: 62 - Forks: 19
murphycj/AGFusion
Python package to annotate and visualize gene fusions.
Language: Python - Size: 345 MB - Last synced at: 16 days ago - Pushed at: 7 months ago - Stars: 61 - Forks: 26
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
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
hall-lab/sv-pipeline
Pipeline for structural variation detection in cohorts
Language: wdl - Size: 941 KB - Last synced at: 1 day ago - Pushed at: over 3 years ago - Stars: 49 - Forks: 20
PacificBiosciences/sawfish
Structural variant discovery and genotyping from mapped PacBio HiFi data
Language: Rust - Size: 693 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 48 - Forks: 2
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
mehrdadbakhtiari/adVNTR
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
Language: Python - Size: 1.42 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 41 - Forks: 15
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
kehrlab/PopDel
Population-wide Deletion Calling
Language: C++ - Size: 20.5 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 35 - 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
tobiasrausch/vc
A tutorial on structural variant calling for short read sequencing data
Language: R - Size: 111 KB - Last synced at: 14 days ago - Pushed at: 6 months ago - Stars: 32 - Forks: 2
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: 17 days ago - Pushed at: over 1 year ago - Stars: 32 - Forks: 1
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: 23 days ago - Pushed at: over 2 years ago - Stars: 32 - Forks: 8
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
ACEnglish/kanpig
Kmer Analysis of Pileups for Genotyping
Language: Rust - Size: 5.01 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 27 - Forks: 1
fritzsedlazeck/SVCollector
Method to optimally select samples for validation and resequencing
Language: C++ - Size: 1.98 MB - Last synced at: 18 days ago - Pushed at: about 4 years ago - Stars: 27 - Forks: 5
PacificBiosciences/SVTopo
Complex structural variant visualization for HiFi sequencing data
Language: HTML - Size: 115 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 26 - Forks: 2
SUwonglab/arcsv
Complex structural variant detection from WGS data
Language: Python - Size: 5.11 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 26 - Forks: 8
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
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
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
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
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
rhshah/iCallSV
A Framework to call Structural Variants from NGS based datasets
Language: Python - Size: 3.12 MB - Last synced at: 23 days ago - Pushed at: over 7 years ago - Stars: 22 - Forks: 10
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
tprodanov/locityper
Targeted genotyper for complex polymorphic genes
Language: Rust - Size: 1.63 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 20 - Forks: 0
edawson/svaha2
Linear-time, low-memory construction of variation graphs
Language: C++ - Size: 609 KB - Last synced at: 2 days ago - Pushed at: about 5 years ago - Stars: 20 - Forks: 0
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
yekaizhou/duet
SNP-Assisted SV Calling and Phasing Using ONT
Language: Python - Size: 2.83 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 18 - Forks: 2
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
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: 22 days ago - Pushed at: 22 days ago - Stars: 16 - Forks: 11
bio-ontology-research-group/DeepSVP
Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity
Language: Python - Size: 843 KB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 16 - Forks: 4
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
ptrebert/project-diploid-assembly
Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data
Language: Jupyter Notebook - Size: 10.9 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 14 - 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: 4 days ago - Pushed at: 4 days ago - Stars: 12 - Forks: 2
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
quanc1989/SV-ONT-Tibetan
Characterization of Structural Variation in Chinese samples
Language: OpenEdge ABL - Size: 108 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 12 - Forks: 7
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
brentp/excord
extract SV signal from a BAM
Language: Go - Size: 18.6 KB - Last synced at: 18 days ago - Pushed at: almost 7 years ago - Stars: 11 - Forks: 1
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: 12 days ago - Pushed at: 12 days ago - Stars: 10 - Forks: 4
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
jeongdo801/scNOVA
scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
Language: R - Size: 56.6 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 3
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
pengsl-lab/SVPath
An accurate pipeline for predicting the pathogenicity of human exon structural variants
Language: Perl - Size: 10.5 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 3
ohdongha/OrthNet
CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology
Language: Python - Size: 176 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 3
vpc-ccg/pamir
Discovery and Genotyping of Novel Sequence Insertions in Many Sequenced Individuals
Language: C++ - Size: 1.79 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 4
frazer-lab/i2QTL-SV-STR-analysis
Code used to process and analyze structural variants and short tandem repeat variants profiled in 719 deeply sequenced whole genomes as part of the i2QTL consortium. This data set consists of sequencing data from the iPSCORE (Frazer lab) and HipSci projects.
Language: Jupyter Notebook - Size: 8.37 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 7 - Forks: 1
brentp/falas
Fragment-Aware Local Assembly for Short-reads
Language: Nim - Size: 20.5 KB - Last synced at: 18 days ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 0
MNMdiagnostics/dbfe
DBFE is a Python library with feature extraction methods that facilitate classifier learning from distributions of genomic variants.
Language: Jupyter Notebook - Size: 48 MB - Last synced at: 12 days ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 3
brentp/bpbio
basepair bio: a single binary with many useful genomics subtools.
Language: Nim - Size: 96.7 KB - Last synced at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 6 - 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
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
phansol/gremlin
GREMLIN: Genomic REarrangements by Machine Learning-based INspection
Language: R - Size: 379 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - 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
NCBI-Hackathons/ScrubSV
A QC pipeline for SVs calls based on coverage and SNP calls
Language: R - Size: 189 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0
tanghaibao/Splithunter
Identify split reads in given chromosomal regions
Language: C++ - Size: 32.6 MB - Last synced at: 18 days ago - Pushed at: over 7 years ago - Stars: 5 - Forks: 1
Han-Cao/collapse-bubble
Merge structural variations (SV) for pangenome VCF
Language: Python - Size: 156 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0
tobiasrausch/sv
Structural variant calling tutorial using long-reads.
Language: R - Size: 55.7 KB - Last synced at: 24 days ago - Pushed at: 3 months ago - Stars: 4 - 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
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
dzyim/List-of-Structural-Variation-Detection-Software
Size: 5.86 KB - Last synced at: 11 days ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1
CarolinaPB/population-structural-var-calling-smoove
population structural variant calling with smoove
Language: Python - Size: 1.84 MB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 3
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
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
fabio-cunial/population-sv-simulator
Studies structural variant callers on large simulated populations sequenced with PacBio CCS
Language: C++ - Size: 9.44 MB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0
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
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
petermchale/denoising_coverage_profiles
Using Convolutional Neural Networks to model an association between a genomic sequence and the number of sequenced reads that align to it
Language: Jupyter Notebook - Size: 44.5 MB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 1
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
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
DanielRivasMD/genomic_structures
Library for interacting with genomic structures, namely mobile elements and structural variants.
Language: Rust - Size: 242 KB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 1 - Forks: 0
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: 23 days ago - Pushed at: 23 days ago - Stars: 1 - Forks: 2
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: about 1 month ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
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: about 1 month ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0
petermchale/trfermikit
Discover VNTR-associated DELs that are hard to find using Illumina reads
Language: Jupyter Notebook - Size: 45.8 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0