Simulation of datasets to assess the impact of sequencing depths, read length, and simulate power
TRUNCATION
The original 50 FASTQ files from Site 1 with a read length of 151 nt were right-truncated to obtain three additional FASTQ files per sample with 50 nt, 75 nt, and 100 nt long reads. Truncation of reads was carried out using the fastx_trimmer tool of the FASTX Toolkit. A set of four FASTQ files per sample to simulate different coverage levels were obtained by randomly down-sampling original reads to 25 million (25 M), 20 million (20 M), 15 million (15 M), and 10 million (10 M) reads. Random subsampling of reads was carried out using the sample tool of the seqtk Toolkit (Version 1.2-r95-dirty). An additional four FASTQ files were simulated for the power analysis using the same approach, which contained 30 M, 40 M, 50 M, and 60 M reads, respectively.