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HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
185 stars 32 forks source link

presets #53

Open HadrienG opened 6 years ago

HadrienG commented 6 years ago

In light of reviewer 3's comments but only vaguely related, it would be a great addition to allow presets of "known" microbiomes to be simulated, i.e.

iss generate --model miseq --preset human_gut --output wathever

I'll get on that after the issues tagged with review though

HadrienG commented 6 years ago

While wanting to create example data, I checked the most abundant git bacteria. Very few of them have a complete genome available.

For having presets we'd need the possibility to consider different contigs to be part of the same bacterium, which is not the case at the moment (the input multifasta is one genome/record)