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yukiteruono / pbsim3

PBSIM3: a simulator for all types of PacBio and ONT long reads
GNU General Public License v2.0
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Sequences Length #7

Closed ChristosMatzoros closed 1 year ago

ChristosMatzoros commented 1 year ago

Hello,

Is there a way to determine the length of the sequences in the generated file? For example to give a minimum or a maximum length?

Regards

yukiteruono commented 1 year ago

Thank you for your using PBSIM.

The length of reads is determined by a gamma distribution with a given mean and SD (--length-mean and --length-sd). The length range can be roughly limited by --length-min and --length-max. In template sequencing mode, the length of reads is approximately the same as the length of templates. In multi-sequencing mode, the length of reads is approximately equal to --length-mean. PBSIM cannot generate a read with exactly the specified length. To do so, simulate reads and then cut them to the length you want.

ChristosMatzoros commented 1 year ago

Thank you