[Bioperl-l] Simulate fragment and read-pair reads from sample sequence

Florent Angly florent.angly at gmail.com
Mon Feb 15 20:19:37 EST 2010

Self-promotion here, but I could not do the things I needed with MetaSim 
and it's not open-source, so I had to roll my own random shotgun library 
simulator: Grinder (http://sourceforge.net/projects/biogrinder/).

Grinder has worked well for my purpose but there's room for 
improvements. Albert, I'd be happy to work with you on adding new 
features in Grinder, for example the mate-pair feature you were mentioning.



On 16/02/10 03:25, Aaron Mackey wrote:
> There are some tools out there that already do a good job of this, and
> take into consideration platform-specific error models, paired end
> fragment length distributions, etc.  maq has an Illumina read
> simulator that also simulates quality scores, and MetaSim has a nice
> 454 read simulator (and Illumina as well, though unfortunately doesn't
> do quality scores for either).

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