Projects in Awesome Lists tagged with structural-variation

https://github.com/fritzsedlazeck/sniffles

Structural variation caller using third generation sequencing

bioconda bioinformatics nanopore ngm-lr pacbio structural-variation structural-variations

Last synced: 14 May 2025

https://github.com/dellytools/delly

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

cancer-genomics delly delly-users genomic germline rearrangement structural-variation sv-discovery svs tumor

Last synced: 21 Oct 2025

https://github.com/Illumina/manta

Structural variant and indel caller for mapped sequencing data

bioinformatics indels structural-variation structural-variations

Last synced: 19 Apr 2025

https://github.com/brentp/smoove

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

genomics lumpy structural-variation

Last synced: 04 Apr 2025

https://github.com/suhrig/arriba

Fast and accurate gene fusion detection from RNA-Seq data

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

Last synced: 21 Jul 2025

https://github.com/broadinstitute/gatk-sv

A structural variation pipeline for short-read sequencing

bioinformatics genomics structural-variants structural-variation

Last synced: 12 Apr 2025

https://github.com/Illumina/paragraph

Graph realignment tools for structural variants

genotyping htslib structural-variation variant-calling vcf

Last synced: 10 May 2025

https://github.com/illumina/paragraph

Graph realignment tools for structural variants

genotyping htslib structural-variation variant-calling vcf

Last synced: 09 Jul 2025

https://github.com/brentp/duphold

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

genomics insanity structural-variation

Last synced: 12 Dec 2025

https://github.com/sbslee/pypgx

A Python package for pharmacogenomics (PGx) research

api cli cyp2d6 genotype pgx pharmacogenetics pharmacogenomics phenotype star-alleles stargazer structural-variation

Last synced: 04 Jan 2026

https://github.com/mehelmy/princess

long-reads methylation phasing single-nucleotide-variation structural-variation

Last synced: 16 Jul 2025

https://github.com/bcgsc/mavis

Merging, Annotation, Validation, and Illustration of Structural variants

bioinformatics genomics python structural-variation transcriptome visualization

Last synced: 08 Sep 2025

https://github.com/tobiasrausch/vc

A tutorial on structural variant calling for short read sequencing data

delly genomics genomics-analysis genomics-visualization structural-variation

Last synced: 29 Oct 2025

https://github.com/smehringer/sviper

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

correction decode-genetics genetics long-reads seqan structural-variation

Last synced: 21 Mar 2025

https://github.com/illumina/witty.er

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

benchmarking cnv copy-number-variation structural-variation variant-analysis variants

Last synced: 10 Apr 2025

https://github.com/tprodanov/locityper

Targeted genotyper for complex polymorphic genes

bioinformatics genomics structural-variation

Last synced: 26 Jan 2026

https://github.com/dellytools/sansa

Structural variant VCF annotation, duplicate removal and comparison

delly gene-annotation structural-variation sv-annotation sv-merging vcf-annotation vcf-comparison vcf-filtering

Last synced: 27 Dec 2025

https://github.com/fritzsedlazeck/svcollector

Method to optimally select samples for validation and resequencing

bioinformatics long-reads ngs ngstools structural-variation vcf

Last synced: 08 Jul 2025

https://github.com/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

annotation cnv cram nextflow-pipeline ngs ngs-pipeline repeats short-reads structural-variation

Last synced: 06 Mar 2026

https://github.com/edawson/svaha2

Linear-time, low-memory construction of variation graphs

genome-graph genomics gfa structural-variation variation-graph

Last synced: 24 Apr 2025

https://github.com/bio-ontology-research-group/deepsvp

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

copy-number-variation ontology structural-variation

Last synced: 25 Jan 2026

https://github.com/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.

annotation python structural-variation

Last synced: 22 Jul 2025

https://github.com/tobiasrausch/nrex

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

alignment germline mutations sequencing somatic-mutations somatic-variants structural-variation variant-calling

Last synced: 10 Jul 2025

https://github.com/brentp/excord

extract SV signal from a BAM

genomics structural-variation

Last synced: 30 Jun 2025

https://github.com/brentp/falas

Fragment-Aware Local Assembly for Short-reads

assembly dna genomics structural-variation

Last synced: 29 Oct 2025

https://github.com/tobiasrausch/sv

Structural variant calling tutorial using long-reads.

delly genomics genomics-analysis structural-variants structural-variation

Last synced: 07 Mar 2026

https://github.com/brentp/bpbio

basepair bio: a single binary with many useful genomics subtools.

bam cram genomics genomics-visualization high-throughput-sequencing structural-variation

Last synced: 28 Jun 2025

https://github.com/tanghaibao/splithunter

Identify split reads in given chromosomal regions

age machine-learning structural-variation t-cell-receptor

Last synced: 22 Aug 2025

https://github.com/barricklab/seabreeze

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

bioinformatics-pipeline experimental-evolution long-read-sequencing structural-variation

Last synced: 03 Apr 2026

https://github.com/morispi/LEVIATHAN

Linked-reads based structural variant caller with barcode indexing

10xgenomics barcodes linked-reads structural-variation svs

Last synced: 14 Mar 2025

https://github.com/acenglish/truvaridata

Data and Scripts relevant to the development and benchmarking of truvari

genomics structural-variation

Last synced: 04 Mar 2026

https://github.com/fabio-cunial/population-sv-simulator

Studies structural variant callers on large simulated populations sequenced with PacBio CCS

bioinformatics-pipeline long-reads sequencing-reads structural-variation

Last synced: 17 Mar 2026

https://github.com/oicr-gsi/delly

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

structural-variation variant-calling workflow

Last synced: 03 Apr 2026

https://github.com/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.

bionano optical-genome-mapping optical-mapping structural-variation structural-variation-calling sv-calling wgs whole-genome-sequencing