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karel-brinda / NanoSim-H

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.
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creating fastq files? #6

Closed nick-youngblut closed 6 years ago

nick-youngblut commented 6 years ago

Is there a way to make fastq files with nanosim-h? It seems to me that it would be preferable to generate fastq versus fasta files, so that nanopore QC software can be run on the fastq files.

karel-brinda commented 6 years ago

Hi Nick, it's not currently possible, sorry for that. Nanosim-h was created as a fork of Nanosim, which lacks this functionality. In my opinion, simulating realistic base qualities is highly non-trivial in the case of nanopore.

nick-youngblut commented 6 years ago

Do you know of any nanopore read simulator that generates fastq (or fast5) files, or does such a tool not exist yet?

karel-brinda commented 6 years ago

I am not currently aware of any simulator that could do that.