Option for number of reads?

[ChristosMatzoros]

Hello,

Is there any option to select the number of created reads as a whole? I use a multi-fasta file as a reference and it seems that pbsim creates an arbitrary number of reads for each FASTA.

Thanks, Chris

[yukiteruono]

Thank you for your using PBSIM2. PBSIM2 does not have an option to select the number of create reads as a whole. You cannot specify the number of reads, but you can use the --depth option to specify the total amount of reads. Simulated reads are randomly sampled from a reference sequence. If the reference is multi-fasta file, the number of reads generated from each reference sequence is roughly proportional to its sequence size.

[ChristosMatzoros]

Thank you