tool simulate paired-end reads and report where each read come from

Question

[Chen Sun]

Hi all,

Could you give me some suggestions for tools that simulate paired-end read data, for each read, the tool will also output the coordinate of genome, where the read comes from.

Right now I use wgsim, but it does not output the coordinate information.

Answer 1

[Istvan Albert]

The name of the read in WGSIM contains the information of where the read originates as well as whether it was mutated or not.

[Chen Sun]

For instance, read gi|157697771|ref|NW_001838433.1|_8301_9008_0:0:0_0:0:0_5cd7, which I simulate from huref chr17.

I known it come from contig gi|157697771|ref|NW_001838433.1, does it mean that 8301 and 9008 are contig coordinate and 0:0:0 talks about mutation, and 5cd7 is read id?

I did not find any document talking about this so I am just not sure.

Thanks

[Istvan Albert]

It is not quite documented but your guess should be close, map the read and also compare the site at a known mutation and you'll get the information from that.