Simulating single end reads with dwgsim

Question

[kautilya]

I am using dwgsim to simulate ion torrent reads. It seems the reads coming from an ion torrent machine are single end. However looking at the commandline options for dwgsim I am unable to see one for generating single end reads. Does anybody know of a way to do this?

Answer 1

[marina.v.yurieva]

Looks like single end is default: -S 0

https://github.com/nh13/DWGSIM/wiki/Simulating-Reads-with-DWGSIM

[kautilya]

I tried the default i.e. -S 0 with -c 2 (for iontorrent) but it still gives me paired end output.