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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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Adds an interactive Jupyter notebook example #350

Closed lebovic closed 1 year ago

lebovic commented 1 year ago

I wrote a notebook based off the real assembly wiki page to help our collaborators get started with MEGAHIT, and thought it might be helpful for others. This PR adds a link to an interactive Jupyter notebook in the README; I'm not sure if that's the best place for this notebook.

To make this work, I built a small service that spins up a unique JupyterLab session for each user and uses our HPC servers for the compute-intensive parts. It's free, can run the real example from the MEGAHIT wiki page in around 20 minutes, and my hope is that it helps researchers get started with MEGAHIT more quickly.

I'm happy to make any changes to the notebook as needed. Here's a short video of the notebook spawning in action:

https://user-images.githubusercontent.com/10551613/218197716-7530c5e6-d8bb-456c-b672-7254cbb3cc68.mov

mmorri commented 1 year ago

this is great, and as a user I would have appreciated to have this while getting started with MEGAHIT

valentynbez commented 1 year ago

Simple tutorial which would lower the entry level for user.