I was just wondering, is there any useful information on wgsim? Tutorial? Anything? I have been stuck with it for the last 2 weeks. I'm really not sure how to use it. I need it for a project of mine. For example, I downloaded a genome from NCBI. What I do is call wgsim like this:
./wgsim -e 0 -s 0 -N 1000 -1 30 -2 30 -r 0 -R 0 -X 0 -A 0 test_genome_one_row.fa read1.fa read2.fa
With this, I would expect that all reads would be the same as the parts of the genome since I set all its error parameters to 0. But somehow, I get reads with mutations(or something else, because they don't belong in the original genome.) What is going on in here and can somebody please explain wgsim's arguments and how can I really control its behaviour? Thanks!