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Search results for structural variation

structural-variation x

89 search results found

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

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

Structural variant and indel caller for mapped sequencing data

Survivor ⭐ 299

Toolset for SV simulation, comparison and filtering

Truvari ⭐ 284

Structural variant toolkit for VCFs

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

Structural variation and indel detection by local assembly

Long read based human genomic structural variation detection with cuteSV

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

Fast and accurate gene fusion detection from RNA-Seq data

New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support

Gatk Sv ⭐ 148

A structural variation pipeline for short-read sequencing

Paragraph ⭐ 140

Graph realignment tools for structural variants

Structurenet ⭐ 121

StructureNet: Hierarchical Graph Networks for 3D Shape Generation

Pipeline Structural Variation ⭐ 87

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

Tools for processing and analyzing structural variants.

Toolkit for calling structural variants using short or long reads

Princess ⭐ 74

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

Merging, Annotation, Validation, and Illustration of Structural variants

Graffite ⭐ 62

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.

Lorikeet ⭐ 61

Strain resolver for metagenomics

simuG: a general-purpose genome simulator

Palimpsest ⭐ 56

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

Bayestyper ⭐ 52

A method for variant graph genotyping based on exact alignment of k-mers

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

Support Vector Structural Variation Genotyper

A Python package for pharmacogenomics (PGx) research

Mumandco ⭐ 49

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

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

Circle Map ⭐ 39

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

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

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

Population-wide Deletion Calling

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

Witty.er ⭐ 26

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

Germline Dna ⭐ 23

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

Identification of segmental duplications in the genome

Aceseqworkflow ⭐ 22

Allele-specific copy number estimation with whole genome sequencing

Sv Pipeline ⭐ 21

Pipeline for structural variation detection in cohorts

Nb_distribution ⭐ 20

novoBreak: local assembly for breakpoint detection in cancer genomes

Complex structural variant detection from WGS data

Kgwasflow ⭐ 19

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

Svcollector ⭐ 17

Method to optimally select samples for validation and resequencing

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

SNP-Assisted SV Calling and Phasing Using ONT

A Framework to call Structural Variants from NGS based datasets

Linear-time, low-memory construction of variation graphs

A straightforward and complete next-generation sequencing read simulator

Allele-Specific Quantification of Structural Variations in Cancer Genomes

Aperture ⭐ 12

Alignment-free detection of structural variations and viral integrations in circulating tumor DNA

Survivor_ant ⭐ 11

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)

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

Sv_benchmark_cmrg ⭐ 10

Structural variant benchmark of challenging medically relevant genes

Iannotatesv ⭐ 10

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

laSV is a software package that employs local assembly to detect structural variations from whole-genome high-throughput sequencing datasets

Identification of structural variations

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

Circle_finder ⭐ 8

Micro DNA identification

A tutorial on structural variant calling for short read sequencing data

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

Project Diploid Assembly ⭐ 8

Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data

Sv Ont Tibetan ⭐ 8

Characterization of Structural Variation in Chinese samples

extract SV signal from a BAM

scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis

A scalable variant calling and benchmarking framework supporting both short and long reads.

Structural variant annotation

a tool for detecting structural variations using soft-clipping information

Simulation toolbox for structural variations.

Upscaling SV detection to a multi-population level.

Location of structural errors in a genome assembly and structural variations between a pair of genomes

Structome ⭐ 6

Toolbox development for structural variations within Irys data retrieved from the BioNano Genomics nick-labeling protocols.

MAMnet uses a deep learning network to call genetic variants from third generation DNA sequencing data.

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

Fragment-Aware Local Assembly for Short-reads

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

The Copasi R connector, a high-level R API for Copasi

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

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

DBFE is a Python library with feature extraction methods that facilitate classifier learning from distributions of genomic variants.

A library for the generation of synthetic data using the Python scientific stack

GREMLIN: Genomic REarrangements by Machine Learning-based INspection

Fast and Accurate Approach of Structural Variations Detection for Short DNA fragments

Svjedi Graph ⭐ 5

SV genotyper for long reads with a variation graph

Hidden Markov Model based Copy number caller

Haplotype Diversity ⭐ 5

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

Splithunter ⭐ 5

Identify split reads in given chromosomal regions

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