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Transposable element detection software tools | Whole-genome sequencing data analysis

Transposable elements (TEs) are dynamic components of genomes that often vary in copy number among members of the same species. With the advent of next-generation sequencing TE insertion-site polymorphism can be examined at an unprecedented level of…
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T-lex
Desktop

T-lex

A software pipeline to analyze transposable elements (TE) insertions in…

A software pipeline to analyze transposable elements (TE) insertions in next-generation sequencing (NGS) data data. T-lex allows users to accurate genotyping of individual TE insertions and get the…

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RetroSeq
Desktop

RetroSeq

A tool for discovery and genotyping of transposable element variants (TEVs)…

A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-generation sequencing reads aligned to a reference genome in BAM…

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MELT
Desktop

MELT Mobile Element Locator Tool

A software package that discovers, annotates, and genotypes non-reference…

A software package that discovers, annotates, and genotypes non-reference mobile element insertions (MEIs) in Illumina DNA paired-end whole genome sequencing (WGS) data. MELT was first conceived as a…

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TEA
Desktop

TEA

A transposable element (TE) analysis pipeline that detects the exact position…

A transposable element (TE) analysis pipeline that detects the exact position and mechanism of TEs insertions from paired-end whole-genome sequencing data with high accuracy. TEA proves that some TE…

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Hydra-sv
Desktop

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.

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EpiTEome
Desktop

EpiTEome

Enables epigenomic investigation of previously overlooked non-reference…

Enables epigenomic investigation of previously overlooked non-reference transposable element (TE) insertion sites. EpiTEome is a Perl package that combines the analysis of new TE insertion sites with…

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VariationHunter
Desktop

VariationHunter

A tool for discovery of structural variation in one or more individuals…

A tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. VariationHunter is now capable of resolving incompatible SV calls through a…

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COSMOS
Desktop

COSMOS

An accurate structural variation (SV) detection method, which compares the…

An accurate structural variation (SV) detection method, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner.…

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TraFiC
Desktop

TraFiC Transposon Finder in Cancer

Uses paired-end sequencing data for the detection of somatic insertions of…

Uses paired-end sequencing data for the detection of somatic insertions of transposable elements (TEs) and exogenous viruses of already known sequence. TraFiC is an in-house pipeline able to identify…

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RelocaTE
Desktop

RelocaTE

Maps transposable elements (TEs) from resequencing data. RelocaTE2 is an…

Maps transposable elements (TEs) from resequencing data. RelocaTE2 is an improved version of RelocaTE for mapping TE insertions to base-pair resolution from resequencing data. This method identifies…

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MAK
Desktop

MAK MITE analysis kit

Facilitates automated analysis of miniature inverted repeat transposable…

Facilitates automated analysis of miniature inverted repeat transposable elements (MITEs). MAK tool kit proposes the following major functions: retrieve the member sequences for a given MITE…

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DD_DETECTION
Desktop

DD_DETECTION

A database-free approach to finding dispersed duplication (DD) events in…

A database-free approach to finding dispersed duplication (DD) events in high-throughput sequencing data. DD_DETECTION is able to detect DDs purely from paired-end read alignments. We show in a…

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TIGRA
Desktop

TIGRA

A computer program that conducts targeted local assembly of structural variants…

A computer program that conducts targeted local assembly of structural variants (SV) using targeted iterative graph routing assembly algorithm. Using data from the 1000 Genomes Project, TIGRA was…

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Mobster
Desktop

Mobster

Detects non-reference mobile element insertions in next generation sequencing…

Detects non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination…

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PTEMD
Desktop

PTEMD Polymorphic TEs and their Movement Detection

A computational method for de novo discovery of genome-wide polymorphic…

A computational method for de novo discovery of genome-wide polymorphic transposable elements (TEs). PTEMD searches highly identical sequences using reads supported breakpoint evidences. It relies on…

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TIF
Desktop

TIF Transposon Insertion Finder

A search program to detect insertions of transposable element from short reads…

A search program to detect insertions of transposable element from short reads of next generation sequencer.

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ProGeRF
Web
Desktop

ProGeRF Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function

Extracts repetitive regions from genome and proteome sequences. ProGeRF was…

Extracts repetitive regions from genome and proteome sequences. ProGeRF was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse…

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TIGER
Desktop

TIGER Transduction Inference in GERmline genomes

Enables the discovery of non-reference LINE-1 (L1)-mediated transductions by…

Enables the discovery of non-reference LINE-1 (L1)-mediated transductions by combining L1 discovery with detection of unique insertion sequences and detailed characterization of insertion sites. By…

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InsertionMapper
Desktop

InsertionMapper

A pipeline tool for the identification of targeted sequences from…

A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. InsertionMapper consists of four independently working modules: data preprocessing,…

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SID
Desktop

SID Specific Insertions Detector

Detects retrotransposon insertion polymorphisms (RIPs). SID is composed of two…

Detects retrotransposon insertion polymorphisms (RIPs). SID is composed of two steps: it detects discordant reads and then clusters reads. It permits to identify non-reference RIPs from whole genome…

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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…

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Jitterbug
Desktop

Jitterbug

Identifies transposable element insertion sites at single-nucleotide resolution…

Identifies transposable element insertion sites at single-nucleotide resolution based on the paired-end mapping and clipped-read signatures produced by NGS alignments. Jitterbug can be easily…

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ISMapper
Desktop

ISMapper

A mapping-based tool for identification of the site and orientation of…

A mapping-based tool for identification of the site and orientation of insertion sequences (IS) in bacterial genomes, direct from paired-end short read data. ISMapper was validated using three types…

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alu-detect
Desktop

alu-detect

Combines read-pair and split-read information to detect novel Alus and their…

Combines read-pair and split-read information to detect novel Alus and their precise breakpoints directly from either whole-genome or whole-exome sequencing data while also identifying insertions…

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McClintock
Desktop

McClintock

Detects transposable element (TE) insertion in next-generation sequencing (NGS)…

Detects transposable element (TE) insertion in next-generation sequencing (NGS) data. McClintock runs automatically and generates standardized output for multiple TE detection methods. McClintock…

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ITIS
Desktop

ITIS Identification of Transposon Insertion Sites

A bioinformatics tool for localizing transposon insertion sites within a…

A bioinformatics tool for localizing transposon insertion sites within a genome. ITIS takes next-generation genome re-sequencing data (NGS data), transposon sequence, and reference genome sequence as…

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TE-locate
Desktop

TE-locate

A tool to locate all copies of sequences in a reference sequence using…

A tool to locate all copies of sequences in a reference sequence using read-pairs.

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Tangram
Desktop

Tangram

A computationally efficient MEI detection program that integrates read-pair…

A computationally efficient MEI detection program that integrates read-pair (RP) and split-read (SR) mapping signals to detect MEI events.

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TE-Tracker
Desktop

TE-Tracker

A general and accurate computational method for the de-novo detection of germ…

A general and accurate computational method for the de-novo detection of germ line Transposable element (TE) mobilization from re-sequenced genomes, as well as the identification of both their source…

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ngs_te_mapper
Desktop

ngs_te_mapper

A software tool for detecting non-reference transposable element insertions…

A software tool for detecting non-reference transposable element insertions from next-generation sequencing data. Non-reference (aka de novo) TE insertions are detected using a two-stage process that…

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RetroPred
Desktop

RetroPred

Allows rapid detection of genomic repeats and their further assignment as LINEs…

Allows rapid detection of genomic repeats and their further assignment as LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements) based on conserve pattern.…

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TEBreak
Desktop

TEBreak

Find and characterise transposable element insertions. TEBreak is a tool for…

Find and characterise transposable element insertions. TEBreak is a tool for analysing insertion mutations. This tool offers any number of variations on the human reference genome. Many additional…

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discord-retro
Desktop

discord-retro

Identifies transposable element (TE) insertions from paired-end whole-genome…

Identifies transposable element (TE) insertions from paired-end whole-genome sequence data, specifically tuned for Illumina reads. There are a number of auxiliary files that specify details of the…

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Visual…
Desktop

Visual ModuleOrganizer

Allows the detection of repeat modules in a set of sequences. Visual…

Allows the detection of repeat modules in a set of sequences. Visual ModuleOrganizer is a Java graphical interface that enables an optimized version of the ModuleOrganizer tool. Visual…

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