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Transposon annotation software tools | De novo genome sequencing data analysis

Repetitive DNA, including transposable elements (TEs), is found throughout eukaryotic genomes. Annotating and assembling the "repeatome" during genome-wide analysis often poses a challenge.Source text:(Goubert et al., 2015) De novo assembly and…
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RepARK
Desktop

RepARK Repetitive motif detection by Assembly of Repetitive K-mers

A de novo repeat assembly method that avoids potential biases by using abundant…

A de novo repeat assembly method that avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome. For validation, repeat consensuses derived from simulated…

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REPdenovo
Desktop

REPdenovo

Assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo…

Assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We…

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TEnest
Web
Desktop

TEnest

Identifies repetitive sequences and reconstructs separated sections to provide…

Identifies repetitive sequences and reconstructs separated sections to provide full-length repeats and, for long-terminal repeat (LTR) retrotransposons, calculates age since insertion based on LTR…

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Tedna
Desktop

Tedna

Assembles a set of transposable elements directly from the reads. Tedna uses…

Assembles a set of transposable elements directly from the reads. Tedna uses Illumina paired-end reads, the most widely used sequencing technology for de novo assembly, and forms full-length…

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TAPDANCE
Desktop

TAPDANCE

Provides a fully automated rationally derived method for complete analysis of…

Provides a fully automated rationally derived method for complete analysis of significant Common Insertion Sites (CISs) using next generation sequencing. TAPDANCE furnishes a pipeline that performs…

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ISQuest
Desktop

ISQuest

Identifies bacterial insertion sequences (ISs) and their sequence…

Identifies bacterial insertion sequences (ISs) and their sequence elements-inverted and direct repeats-in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs…

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Transposome
Desktop

Transposome

A command line application to annotate transposable elements from paired-end…

A command line application to annotate transposable elements from paired-end whole genome shotgun data. There are many tools to estimate the mathematical nature of repeats from short sequence reads.…

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dnaPipeTE
Desktop

dnaPipeTE

A bioinformatic pipeline dedicated to find, annotate and quantify transposable…

A bioinformatic pipeline dedicated to find, annotate and quantify transposable elements as well as other repeated DNA, in NGS low coverage genomic datasets. dnaPipeTE produces a global estimation of…

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RepeatExplorer
Web

RepeatExplorer

A collection of software tools for characterization of repetitive elements,…

A collection of software tools for characterization of repetitive elements, which is accessible via web interface. A key component of the server is the computational pipeline using a graph-based…

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