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dib-lab / 2021-paper-metapangenomes

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Add tessa's changes, clean up comments/signposting, missing citations, and add abstract #10

Closed taylorreiter closed 2 years ago

taylorreiter commented 2 years ago

The biggest things this PR does is:

  1. address comments Tessa provided on the manuscript, including simplifying the first section to only include protein k-mers, instead of protein, hayhoff, and hp. We didn't explore dayhoff and hp much, so I took that bit out. (although I did leave the supplemental figure as is...I could cut that down to only protein as well)
  2. adds an abstract

@ctb & @bluegenes ready for review. I would love if you could comment that you have seen this pull request and you are ok with the changes.

After this is merged in, and if there are no other immediate changes, I plan to send it along to the other co-authors for approval.

Once everything is approved by all co-authors, I'll generate zenodo DOIs for the companion analysis repositories & update the manuscript to reference them, update the citation to Tessa's research with a url to a draft of her paper, dump the abstract and title in the README of this repo, and transfer the repo to DIB lab. Then I think we will be ready to preprint!

I will also update the citations to charcoal, the IBD paper, and Tessa's paper once those are preprinted.

taylorreiter commented 2 years ago

Thanks @ctb! i've committed your changes

taylorreiter commented 2 years ago

Thank you both! merging now.