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Home modified by Robert Kofler

Robert Kofler — Mon, 27 Nov 2017 10:49:16 -0000

--- v42
+++ v43
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 * [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

Home modified by Robert Kofler

Robert Kofler — Mon, 09 Oct 2017 12:52:05 -0000

--- v41
+++ v42
@@ -25,7 +25,7 @@
 * [Manual]
 * [describing_TE_landscapes]
 * [describing_TE_sequences]
-* [special_use_cases]  (solo-LTRs, 5' truncated non-LTRs, internally truncated TIRs, diverged TE sequences, etc)
+* [special_use_cases]  advanced section demonstrating how to generate solo-LTRs, 5' truncated non-LTRs, internally truncated TIRs, diverged TE sequences, etc

Home modified by Robert Kofler

Robert Kofler — Mon, 09 Oct 2017 12:02:09 -0000

--- v40
+++ v41
@@ -25,6 +25,7 @@
 * [Manual]
 * [describing_TE_landscapes]
 * [describing_TE_sequences]
+* [special_use_cases]  (solo-LTRs, 5' truncated non-LTRs, internally truncated TIRs, diverged TE sequences, etc)

Home modified by Robert Kofler

Robert Kofler — Mon, 09 Oct 2017 09:30:55 -0000

Home modified by Robert Kofler

Robert Kofler — Mon, 09 Oct 2017 09:30:44 -0000

Home modified by Robert Kofler

Robert Kofler — Mon, 09 Oct 2017 08:40:43 -0000

Home modified by Robert Kofler

Robert Kofler — Fri, 28 Jul 2017 13:22:37 -0000

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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 grammar**. 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.
+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:

Home modified by Robert Kofler

Robert Kofler — Fri, 28 Jul 2017 13:22:01 -0000

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+++ v36
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 [TOC]

 #SimulaTE#
-SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all 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.
+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 grammar**. 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.

Home modified by Robert Kofler

Robert Kofler — Tue, 25 Jul 2017 13:03:59 -0000

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 # 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 for TE identification in populations
+* [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

Home modified by Robert Kofler

Robert Kofler — Tue, 25 Jul 2017 13:02:48 -0000

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 # 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
-* [Walkthroug_species_tool_compatibility]: evaluate the suitability of given genomic resources for TE identification in populations
+* [Walkthrough_species_tool_compatibility]: evaluate the suitability of given genomic resources for TE identification in populations
 * [Walkthrough_toy] test the behaviour of SimulaTE using simple toy examples

 # Validation