TEMP2: an algorithm for detecting germline and de novo transposon insertions using short-read whole-genome sequencing data
Transposons are genomic parasites, and their new insertions can cause instability and spur the evolution of their host genomes. Rapid accumulation of short-read whole-genome sequencing data provides a great opportunity for studying new transposon insertions and their impacts on the host genome. Although many algorithms are available for detecting transposon insertions, the task remains challenging due to the repetitive nature of transposon sequences and the lack of gold standard datasets for benchmarking the algorithms. Furthermore, existing tools are not designed for identifying the de novo insertions, which can be generated during development or due to defects in the silencing machinery, and are generally represented by single read pairs. Here we present a new gold-standard fly dataset based on PacBio long-read sequencing and a new method TEMP2 for detecting fixed germline insertions and de novo “singleton” insertions in eukaryotic genomes. TEMP2 achieves high sensitivity and precision for detecting germline insertions when compared with existing tools using both simulated data in fly and experimental data in fly and human. Furthermore, TEMP2 can accurately assess the frequencies of de novo transposon insertions even with high levels of chimeric reads in simulated datasets; such chimeric reads often occur during the construction of short-read sequencing libraries. By applying TEMP2 to published data on hybrid dysgenic flies inflicted by depressed P-elements, we confirmed the continuous new insertions of P-elements in dysgenic offspring before they regain piRNAs for P-element repression. TEMP2 is freely available at Github: https://github.com/weng-lab/TEMP2. Overall design: Pacbio and Illumina sequencing of ISO-1 D. melanogaster genome