From prokaryotes to eukaryotes, phenotypic variation, adaptation and speciation has been associated with structural variation between genomes of individuals within the same species. Many computer algorithms detecting such variations (callers) have recently been developed,…
Desktop app
G T A T C G C T A Hydra-sv Hydra-sv

Hydra-sv

Detects structural variation (SV) breakpoints by clustering discordant…

Detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose "signatures" corroborate the same putative breakpoint.

Desktop app
G T A T C G C T A SVMerge SVMerge

SVMerge

A pipeline to detect structural variants (SVs) by integrating calls from…

A pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly.

Desktop app
G T A T C G C T A APOLLOH APOLLOH

APOLLOH

A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and…

A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

Desktop app
G T A T C G C T A FusionMap FusionMap

FusionMap

An efficient fusion aligner which aligns reads spanning fusion junctions…

An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions.

Desktop app
G T A T C G C T A nFuse nFuse

nFuse

Predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole…

Predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

Desktop app
G T A T C G C T A Breakpointer Breakpointer

Breakpointer

A fast tool for locating sequence breakpoints from the alignment of single end…

A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS).

Desktop app
G T A T C G C T A WHole-genome… WHole-genome Alignment Metrics

Wham WHole-genome Alignment Metrics

A structural variant (SV) caller that integrates several sources of mapping…

A structural variant (SV) caller that integrates several sources of mapping information to identify SVs. Wham classifies SVs using a flexible and extendable machine-learning algorithm (random…

Desktop app
G T A T C G C T A Genomic Rearrangement… Genomic Rearrangement IDentification Software…

GRIDSS Genomic Rearrangement IDentification Software Suite

Calls variants based on alignment-guided positional de Bruijn graph break-end…

Calls variants based on alignment-guided positional de Bruijn graph break-end assembly, split read, and read pair evidence. GRIDSS is a modular breakend assembler and structural variation caller for…

Desktop app
G T A T C G C T A RawGeno RawGeno

RawGeno

Proceeds to the binning and scoring of amplified fragmen-length polymorphisms…

Proceeds to the binning and scoring of amplified fragmen-length polymorphisms (AFLP) electropherograms. RawGeno includes several filters to assess the quality of electropherograms and checks the…

Desktop app
G T A T C G C T A novoBreak novoBreak

novoBreak

A tool to generate local assemblies of breakpoints genome-wide. NovoBreak is an…

A tool to generate local assemblies of breakpoints genome-wide. NovoBreak is an algorithm used in cancer genomic studies to discover structural variants (both somatic and germline) breakpoints in…

Desktop app
G T A T C G C T A targetSeqView targetSeqView

targetSeqView

A probability-based score and visualization method to aid in distinguishing…

A probability-based score and visualization method to aid in distinguishing true structural variants from alignment artifacts. targetSeqView is able to separate real structural variants from false…

Desktop app
G T A T C G C T A Hydra-Multi Hydra-Multi

Hydra-Multi

A paired-end read structural variant discovery tool that is capable of…

A paired-end read structural variant discovery tool that is capable of integrating signals from hundreds of samples. Given the increasing number of large-scale genome sequencing projects, the rapid…

Desktop app
G T A T C G C T A Ulysses Ulysses

Ulysses

A tool that achieves drastically higher detection accuracy than existing tools,…

A tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high…

Desktop app
G T A T C G C T A Paired-end… Paired-end Reconstruction of Genome Organization

PREGO Paired-end Reconstruction of Genome Organization

An algorithm that reconstructs a cancer genome as a rearrangement of segments,…

An algorithm that reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired-end sequencing data. PREGO identifies complex and biologically…

Desktop app
G T A T C G C T A MultiBreak-SV MultiBreak-SV

MultiBreak-SV

Recent "third-generation" sequencing technologies provide…

Recent "third-generation" sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. MultiBreak-SV…

Desktop app
G T A T C G C T A hot_scan hot_scan

hot_scan

A free software to detect genomic regions unusually rich in translocation…

A free software to detect genomic regions unusually rich in translocation breakpoints.

Desktop app
G T A T C G C T A SquareDancer SquareDancer

SquareDancer

This tool identifies SVs or splice junctions from soft-clipped genomic or cDNA…

This tool identifies SVs or splice junctions from soft-clipped genomic or cDNA reads.

Desktop app
G T A T C G C T A BreakTrans BreakTrans

BreakTrans

A computer program that maps predicted gene fusions to genomic structural…

A computer program that maps predicted gene fusions to genomic structural rearrangements so as to validate both types of events and provide them mechanism/functional interpretation.

Desktop app
G T A T C G C T A SlideSort-BPR SlideSort-BPR

SlideSort-BPR

A reference-free method for detecting clusters of breakpoints from the…

A reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.

Desktop app
G T A T C G C T A Socrates Socrates

Socrates

A method for detecting genomic rearrangements in tumours that utilises only…

A method for detecting genomic rearrangements in tumours that utilises only split-read data.

Desktop app
G T A T C G C T A BreakSeq BreakSeq

BreakSeq

Database of known human breakpoint junctions and software to search short reads…

Database of known human breakpoint junctions and software to search short reads against them.

Desktop app
G T A T C G C T A deStruct deStruct

deStruct

A software tool for identifying structural variation in tumour genomes from…

A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.

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