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davidebolo1993 / VISOR

VarIant SimulatOR for short, long and linked reads
GNU Lesser General Public License v3.0
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Feature Request: Add --length-max option #12

Closed tjiangHIT closed 3 years ago

tjiangHIT commented 3 years ago

Hello @davidebolo1993

VISOR uses pbsim to perform long-read simulation, and the default maximum length of read is 25 kbp (CLR). It seems enough for the practice of generating long-read which mean length smaller than 25 kbp. However, when simulate long-reads which the mean read length over 25 kbp, an error will be raised by the maximum length in pbsim. Moreover, this default maximum length is not in accordance with the real long-read sequencing technologies, where the longest read length has achieved over 100 kbp. So it would be of great help that add a new --length-max option in order to set the maximum length of long-reads.

Thank you. Tao

davidebolo1993 commented 3 years ago

Hi @tjiangHIT,

I've added the --maxlength, --minlength and --sdlength parameters to VISOR LASeR for the fine tuning of long-read simulations. This should work. Feel free to reopen if I missed something.

Cheers,

Davide

davidebolo1993 commented 3 years ago

Hi @tjiangHIT,

the new version of VISOR uses Badread for simulations. I've tested cuteSV on simulated data and it works fine. Maybe you want to have a look for yourself.

Best,

Davide

tjiangHIT commented 3 years ago

Hi @tjiangHIT,

the new version of VISOR uses Badread for simulations. I've tested cuteSV on simulated data and it works fine. Maybe you want to have a look for yourself.

Best,

Davide

Great News! I'll check. Best, Tao