filename of reference sequence (FASTA) : CAEC_viral.fasta  
filname of the aligned reads (sam format) : CAEC_viral.sam
SNP_thres (0.5 / ploidy for haplotype assembly and 0.01 for viral quasispecies) : 0.01
reconstruction_start : 1
reconstruction_stop : 5000
min_mapping_qual : 60
min_read_length : 70
max_insert_length : 3000
characteristic zone name : CAEC_viral
Initial population size : 3
Number of experiments : 10
Which GPU to use (set to -1 if only use CPU; otherwise set to 0, 1, 2 or 3 ... if multiple GPUs are available; check instructions for details) : 1
MEC improvement threshold(This is used for viral quasispecies reconstruction) : 0.09