Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Intra-chromosomal translocation detection software tools | Whole-genome sequencing data analysis

G T A T C G C T A
SV-STAT
Desktop

SV-STAT Structural Variation detection by STAck and Tail

Quantifies evidence for structural variation in genomic regions suspected of…

Quantifies evidence for structural variation in genomic regions suspected of harboring rearrangements. SV-STAT extends existing methods by adjusting a chimeric read’s support of a structural…

G T A T C G C T A
FACTERA
Desktop
G T A T C G C T A
BreakDancer
Desktop

BreakDancer

A Perl/C++ package that provides genome-wide detection of structural variants…

A Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancer sensitively and accurately detected indels ranging from 10…

G T A T C G C T A
CREST
Web

CREST Clipping REveals STructure

An algorithm using NGS reads with partial alignments to a reference genome to…

An algorithm using NGS reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level. Application of CREST to whole-genome sequencing data from…

G T A T C G C T A
Meerkat
Desktop

Meerkat

To characterize the mutational spectrum of somatic SVs in cancer, it is…

To characterize the mutational spectrum of somatic SVs in cancer, it is important to identify both simple (e.g., deletion, insertion, and inversion) and complex SVs at base-pair resolution. Meerkat…

G T A T C G C T A
DELLY
Desktop

DELLY

An integrated structural variant prediction method that can detect deletions,…

An integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel…

G T A T C G C T A
PSSV
Desktop

PSSV

A probabilistic method for somatic structural variation (SV) prediction by…

A probabilistic method for somatic structural variation (SV) prediction by jointly modeling discordant and concordant read counts. PSSV is specifically designed to predict somatic deletions,…

G T A T C G C T A
Breakway
Desktop

Breakway

A suite of programs that take aligned genomic data and report structural…

A suite of programs that take aligned genomic data and report structural variation breakpoints.

G T A T C G C T A
SVDetect
Desktop

SVDetect

A tool to detect genomic structural variations from paired-end and mate-pair…

A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.

G T A T C G C T A
GROM
Desktop

GROM Genome Rearrangement OmniMapper

Allows variant detection, combining mismatch, split-read, read pair, and read…

Allows variant detection, combining mismatch, split-read, read pair, and read depth whole genome sequence (WGS) evidence. GROM is able to detect single nucleotide variants (SNVs), indels, structural…

G T A T C G C T A
Sniffles
Desktop

Sniffles

Provides a structural variation (SV) caller for long reads. Sniffles is mainly…

Provides a structural variation (SV) caller for long reads. Sniffles is mainly designed for PacBio reads, but also works on Oxford Nanopore reads. SV are larger events on the genome (e.g. deletions,…

G T A T C G C T A
SLOPE
Desktop

SLOPE

Detects structural variants from targeted short-DNA reads. Both real and…

Detects structural variants from targeted short-DNA reads. Both real and simulated data are used to demonstrate SLOPE's ability to rapidly detect insertion/deletion events of various sizes as…

G T A T C G C T A
BreaKmer
Desktop

BreaKmer

An approach that uses a 'kmer' strategy to assemble misaligned…

An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair…

G T A T C G C T A
GROC-SVs
Desktop

GROC-SVs Genome-wide Reconstruction of Complex Structural Variants

Identifies structural variants, performs sequence assembly at the breakpoints,…

Identifies structural variants, performs sequence assembly at the breakpoints, and reconstructs the complex structural variants using the long-fragment information from the 10x Genomics platform.…

G T A T C G C T A
SV-Bay
Desktop

SV-Bay

Detects structural variants in cancer using whole genome sequencing data with…

Detects structural variants in cancer using whole genome sequencing data with or without matched normal control sample. SV-Bay does not only use information about abnormal read mappings but also…

G T A T C G C T A
Manta
Desktop

Manta

Calls structural variants (SVs) and indels from mapped paired-end sequencing…

Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta is optimized for analysis of individuals and tumor/normal sample pairs, calling SVs, medium-sized indels and…

G T A T C G C T A
MetaSV
Desktop

MetaSV

An integrated structural variation (SV) caller which leverages multiple…

An integrated structural variation (SV) caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of…

G T A T C G C T A
SV-AUTOPILOT
Desktop

SV-AUTOPILOT Structural Variation AUTOmated PIpeLine Optimization Tool

Standardizes the Structural Variation (SV) detection pipeline. SV-AUTOPILOT is…

Standardizes the Structural Variation (SV) detection pipeline. SV-AUTOPILOT is a pipeline that can be used on existing computing infrastructure in the form of a Virtual Machine (VM) Image. It…

G T A T C G C T A
MUMdex
Desktop

MUMdex Maximal Unique Matchdex

A package for aligning sequences to a reference genome. MUMdex consists of an…

A package for aligning sequences to a reference genome. MUMdex consists of an aligner, an alignment format, an analysis software and a portable population database of common structural variants to…

G T A T C G C T A
Gustaf
Desktop

Gustaf Generic mUlti-SpliT Alignment Finder

A sound generic multi-split SV detection tool that detects and classifies…

A sound generic multi-split SV detection tool that detects and classifies deletions, inversions, dispersed duplications and translocations of >/=30 bp.

G T A T C G C T A
SVmine
Desktop

SVmine

Employs a two-stage process to evaluate and refine structural variation (SV)…

Employs a two-stage process to evaluate and refine structural variation (SV) predictions. SVmine is an algorithm for further mining of SV predictions from multiple algorithms to improve the…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.