structural-variation
There are 16 repositories under structural-variation topic.
fritzsedlazeck / Sniffles
Structural variation caller using third generation sequencing
Language:Python 515dellytools / delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Language:C++ 403- Language:C++ 388
- truvariLanguage:Python 294
- Language:Python 232
- Language:Go 221
- Language:C++ 210
broadinstitute / gatk-sv
A structural variation pipeline for short-read sequencing
Language:Python 159- Language:C++ 145
- Language:Python 142
nanoporetech / pipeline-structural-variation
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Language:Python 110- Language:Nim 99
bioinformatics-centre / BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
Language:C++ 86- Language:Cython 86
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 84- Language:Perl 83
- Language:Python 79
- Language:Python 72
FunGeST / Palimpsest
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
Language:R 69- ClinSV
KCCG / ClinSV
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
Language:Perl 61 iprada / Circle-Map
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
Language:Python 60- MUMandCo
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 59 - Language:Python 58
- Language:Python 57
- Language:Python 54
XiaoTaoWang / NeoLoopFinder
A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
Language:Python 51hall-lab / sv-pipeline
Pipeline for structural variation detection in cohorts
Language:wdl 45- Language:C++ 45
Kingsford-Group / squid
SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
Language:C++ 40mehrdadbakhtiari / adVNTR
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
Language:Python 38- Language:C++ 33
Oshlack / MINTIE
Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
Language:Python 33smehringer / SViper
Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.
Language:C++ 32Method to optimally select samples for validation and resequencing
Language:C++ 26Illumina / witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
Language:C# 26- Language:C++ 26
