input file

[shrukane]

Hi,
First, thank you for writing this package, a simulator serves a lot of purposes !
I'm trying to simulate paired end ddRAD data for practice testing different pipelines and I have a couple of questions. What type of input does simrrls use ? and what is the option for the input ?
Does the tool simulate SNPs? if yes, how would u know where they are?

Regards
Shruti

[dereneaton]

Hi Shruti,

simrrls takes parameter arguments to simulate RADseq data, and then simulates data either on a balanced 12 taxon tree (default), or an input tree if you provide one. The output is formatted as raw fastq files which can then be assembled using the software ipyrad (https://github.com/dereneaton/ipyrad/), which will isolate the SNPs for you.