I think it may be helpful to throw an example into Jupyter notebook and link to it (or https://docs.readthedocs.io/en/stable/guides/jupyter.html)
Especially since the tutorial jumps around between running things on command line and python
[ ] Benchmarking Example
[ ] Exploring a metagenome/binning using Autometa imports
Additional code snippets could be added using the autometa api located on autometa.readthedocs.io under Autometa python API
[ ] Quickly determining a set of contigs' bin metrics
[ ] Quickly retrieving a set of taxids lineages (including both canonical and non-canonical ranks)
[ ] Some parameter sweep workflows regarding kmers or binning (maybe tying in benchmarking from above?)
I think it may be helpful to throw an example into Jupyter notebook and link to it (or https://docs.readthedocs.io/en/stable/guides/jupyter.html) Especially since the tutorial jumps around between running things on command line and python
Additional code snippets could be added using the autometa api located on autometa.readthedocs.io under Autometa python API
Originally posted by @chasemc in https://github.com/KwanLab/Autometa/issues/189#issuecomment-933430269