2.5 | Simulation of ancient DNA reads
To investigate the efficacy of the optimized in silico method in regard to genome assembly of extinct species with ancient DNA, we simulated ancient DNA reads. We chose the cleaned data of T. flavidus to simulate ancient DNA data because it is a high-quality genome assembly generated using both mate-pair sequencing and PacBio sequencing. After correction, the forward strand of paired-end reads (insert size of 250 bp, read length 150 bp) was cut at a random length to form 80 bp to 100 bp single-end reads using an in-house python script (Simulate.py). The size distribution of the simulated reads is shown (Fig. S1). For simulated ancient DNA, genomes of T. rubripes(same genus), T. bimaculatus (same genus), T. nivigroviridis (same family), and M. mola (same order) were selected as references. The statistics of these references are summarized (Table S6).