Read Simulation: reference length limitation? about nanosim

[cheny19]

NanoSim is able to deal with multiple entries in a fasta file and it should work fine for small reference genomes, just take longer to generate a proper read length. Could you send me your reference plasmid fasta file so I can test on it? Thanks!

[ampodu]

I send the file to your bcgsc.ca mail address.

I did some more testing and it seems that every reference over ~40kb works but with ~20kb or less it always crashes for me. However, if I use --perfect, it works just fine. The problem probably lies within mutate_read.

[ampodu]

I found a solution: specifying the "max_len" as the length of the reference contigs.
Seems like it was trying to create reads longer than the reference?

[cheny19]

Oh, I see. NanoSim will try to mimic the length distribution as the training profile. So if your reference genome is smaller than the empirical length distribution, it may not able to find the right length for each read. Specifying the max_len is the solution and probably you don't mind the simulated read length doesn't mach the profile given the reference size.