output different replicates of a sample

bcgsc / NanoSim

Nanopore sequence read simulator

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output different replicates of a sample #214

Closed zzare-umd closed 3 months ago

zzare-umd commented 3 months ago

Hi,

Thank you for providing such a great software tool. I am currently using NanoSim to simulate an ONT cDNA dataset from a FASTQ file. I would like to generate different replicate samples. Can this be achieved by changing the "seed" value during the simulation?

Regards, Zahra

lcoombe commented 3 months ago

Hi Zahra,

Running NanoSim multiple times with the same settings (except for using a different output prefix, of course) will yield different simulated read sets. NanoSim samples from various distributions, and is not deterministic. You can verify this by running abyss-fac or a similar utility on the simulated reads, and will see that their N50, sum, max length, etc. should be non-identical.

Thank you for your interest in NanoSim! Lauren