#algorithmicbioinformatics peeps!
Say, hypothetically, I wanted to test a new read mapper/pairwise aligner for Nanopore reads.
For synthetic reads, what is the length and error-rate I should aim for, and is there a specific tool to simulate Nanopore reads (I'm using pbsim with 10% and 25kb right now, and I'm aware of nanosim, though I'd like to use something simpler, if it exists)?
For real data, what's the most current read set (and reference) people like to use for benchmarking?
Thanks!
@baris If you want to test the aligner’s performance on low quality reads, you can use Badread. (https://github.com/rrwick/Badread) The creator of this program also wrote an article comparing the common read simulators. (https://github.com/rrwick/Badread/tree/main/comparison)
