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.

Manual https://sourceforge.net/p/simulates/wiki/Home/#manual
Walkthrough https://sourceforge.net/p/simulates/wiki/Home/#walkthrough
Validation https://sourceforge.net/p/simulates/wiki/Home/#validation