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SimulaTE

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of the indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.
As major innovation we developed a simple Domain Specific Language (DSL) that allows to specify arbitrary complex TE landscapes using a simple syntax. A DSL is a custom tailored programming language that is optimized for a specific purpose, i.e. in the case of SimulaTE describing TE landscapes.

The DSL implemented in SimulaTE allows to specify the following properties of TE landscapes:

• positions of insertions
• family
• strand
• TSD (target site duplication)
• population frequency
• haplotype of TE insertions
• sequence divergence
• truncations
• nested insertions
• recursively nested insertions

Manual

• [Manual]
• [describing_TE_landscapes]
• [describing_TE_sequences]
• [special_use_cases] advanced section demonstrating how to generate solo-LTRs, 5' truncated non-LTRs, internally truncated TIRs, diverged TE sequences, etc

Walkthrough

• [Walkthrough] a quick introduction: generate TE landscapes and simulate reads
• [TheClassic_SanMiguel_TELandscape] create the classic TE landsape described by SanMiguel et al. (1996) using SimulaTE ; validate the result with RepeatMasker
• [Walkthrough_species_tool_compatibility]: evaluate the suitability of given genomic resources or a given approach for TE identification
• [Walkthrough_toy] test the behaviour of SimulaTE using simple toy examples

Validation

• [TheClassic_SanMiguel_TELandscape] create the classic TE landsape described by SanMiguel et al. (1996) using SimulaTE ; validate the result with RepeatMasker
• [Validation_Pop2] simulate a complex TE landscape for a population and validate the position as well as the population frequency of the TE insertions using PoPoolation TE2.
• [Validate_reads] validate the scripts simulating Illumina and PacBio reads
• [Validate_unit_tests] run the unit-tests which ensure proper function of our DSL for describing complex TE landscapes

Cite

• Robert Kofler (2017) SimulaTE: Simulating complex landscapes of transposable elements of populations; Bioinformatics https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btx772/4665422

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Project Members:

• Robert Kofler (admin)