structural-variants

There are 2 repositories under structural-variants topic.

broadinstitute / gatk-sv
A structural variation pipeline for short-read sequencing
genomics structural-variants structural-variation bioinformatics
Language:Python 162
MoMI-G / MoMI-G
Modular Multi-scale Integrated Genome Graph Browser
genome-browser genome-graph graph-genome-browser structural-variants variation-graph
Language:TypeScript 85
nf-core / raredisease
Call and score variants from WGS/WES of rare disease patients.
nf-core nextflow workflow pipeline wgs wes variant-calling snv structural-variants variant-annotation diagnostics rare-disease
Language:Nextflow 75
GooglingTheCancerGenome / sv-callers
Snakemake-based workflow for detecting structural variants in genomic data
bioinformatics cancer-genomics germline-variants hpc-applications snakemake somatic-variants structural-variants sv-calling wgs workflow
Language:Python 73
HiPhase
PacificBiosciences / HiPhase
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
hifi pacbio-data phasing short-tandem-repeats structural-variants variants
Language:Rust 56
GATB / MindTheGap
MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.
bioinformatics debruijn-graph gatb genomics structural-variants
Language:C++ 35
vicsanga / Postre
POSTRE: Prediction Of STRuctural variant Effects
copy-number-variation medical-genetics non-coding-variants structural-variants cnvs pathogenic-variants pathogenicity
Language:R 19
bcgsc / pavfinder
:mag: Post Assembly Variants Finder
assembly bioinformatics gene-fusions rna-seq splice-variants structural-variants
Language:Python 17
OpenOmics / genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
copy-number-variation germline-variants quality-control structural-variants singularity snakemake whole-genome-sequencing somatic-variants pipeline hla-typing variant-annotation variant-effect-prediction whole-exome-sequencing
Language:Python 17
WGLab / PhenoSV
PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.
phenotyping structural-variants transformer variant-interpretation
Language:Python 14
GooglingTheCancerGenome / sv-gen
Snakemake-based workflow for generating artificial genomes with structural variants
bioinformatics cancer-genomics hpc-applications simulator snakemake structural-variants wgs workflow
Language:Python 6
nf-core / variantbenchmarking
A nextflow variant benchmarking pipeline - premature
benchmark draft variant-calling structural-variants nextflow nf-core pipeline workflow
Language:Nextflow 6
dbespiatykh / RDscan
A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples
bioinformatics snakemake mycobacterium mycobacterium-tuberculosis-complex structural-variants bacterial-genome-analysis mycobacterium-tuberculosis
Language:Python 5
smail-lab-cmh / ga4k-sv-finder
Long read structural variants in rare disease cohort
allele-frequencies long-read structural-variants wgs
Language:Python 4
Sydney-Informatics-Hub / Germline-StructuralV-nf
Germline structural variant calling pipeline for short read WGS datasets
australian-biocommons bam bioinformatics dsl2 germline-variant-calling manta nextflow ngs pipeline smoove structural-variants survivor tiddit workflow annotsv genomics
Language:Nextflow 4
xjtu-omics / ChineseQuartetGenome
Genome assembly and variant benchmarks for Chinese Quartet
genome-assembly chinese-quartet variant-benchmark indel snv haplotype-resolved-assembly structural-variants
Language:Python 3
jasonwong-lab / smk_sv
A snakemake pipeline to call structure variants from ONT data
long-read-sequencing oxford-nanopore-sequencing structural-variants structural-variation-calling bioinformatics bioinformatics-pipeline structural-variations
Language:Python 2
NonRoute / Bioinformatic-I-Project
2110581 Bioinformatics I project - Structural variant detection
bioinformatics structural-variants
Language:Jupyter Notebook 2
auroramaurizio / my_DNA_seq_pipelines
In this repository I backup the pipelines I write for the project I am involved
cnv contamination-detection dna-sequencing snv tas wes wgs plots vaf variant-calling purity structural-variants
Language:Python 1
Hynst / WTS_cSVs_analysis
rna-seq bioinformatics-analysis structural-variants
Language:R 1
ITBE-Lab / MSV-EVAL
The experiments performed in State-of-the-art structural variant calling: What went conceptually wrong and how to fix it?
bioinformatics pan-genome structural-variants
Language:Python 1
leahkemp / test_SV_callers
Testing structural variant (SV) callers for illumina germline whole genome sequence (WGS) data (human).
illumina structural-variants whole-genome-sequencing
Language:Shell 1
bdolmo / GRAPES
Integrated analysis of Structural and Copy Number Variants on clinical targeted sequencing data
cnv gene-panels structural-variation structural-variants
Language:Perl 0
d-fuh / Garvan_summerproject2021
Garvan KCCG Student Summer Research Project #1 Benchmarking structural variant callers on whole genome sequencing data
genomics structural-variants structural-variation-calling
Language:R 0
LupienLab / 3d-reorganization-prostate-cancer
Code, analysis, and results for Hawley, Zhou, et al., Cancer Research, 2021.
bioinformatics 3d-genome prostate-cancer structural-variants
Language:HTML 0
drvenki / sv-cfdna
Structural Variants in cell-free tumor DNA
liquidbiosy cfdna cellfreedna cellfree ctdna circulatingtumordna structural-variation structural-variants cf-dna ct-dna cell-free-dna circulating-tumor
LitianZhou / litianzhou-pf-sv
My work during internship in Walter+Eliza Hall Institute of Medical Research
structural-variants plasmodium sniffles
Language:HTML
TheJacksonLaboratory / SV_Paired_BAM_NXF
Pipeline to analyze structural variants producing VCF files, then merge them and annotate if in Exon.
analysis structural-variants vcf-files pipeline nextflow
Language:Nextflow