Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

[kevinlibuit]

No description provided.

[whedon]

👋 This repository is only for review issues (pre-review and review) that have been created by our editorial infrastructure, and this issue appears not to be one of these.

As such, this issue will be closed. If you're opening an issue as part of a review, please open a new issue instead in the software repository associated with the submission that you are reviewing.

Many thanks!

[kevinlibuit]

RE: Nextalign was written for a very specific use case: fast pairwise alignment of similar sequences (< 10% divergence) with limited insertions and deletions.

I use this tool quite often for SC2 sample characterization and can say, subjectively, that it certainly performs fast pairwise alignment. For this manuscript, however, are there data that can be included to support/demonstrate the quantification of its speed?

[kthyng]

@kevinlibuit Hi! The little automatic issue-creator buttons in github unfortunately don't work with the JOSS workflow. Please delete this and move your note to an issue created in the software repository, and link it back to the review issue. Let me know if you have any questions.

[kevinlibuit]

Whoops! Thanks for the heads up. I saw the instructions to create issues on the repo itself, but got confused when I saw the button to create issues on the checklist itself.

Thanks, @kthyng

[kevinlibuit]

Is it appropriate to add those comments to the public repo? This is more so a comment on the article and its performance claims. I'll just add this to the convo on the review page.

[kthyng]

@kevinlibuit Sure, if it is a small comment, you may want to have a summary of small comments on the review issue itself. For items you want addressed (like maybe your question above?), put them in an issue in the software itself (here: https://github.com/nextstrain/nextclade/issues) with a link to the review issue (#3773) so that they can be addressed one by one — just helps with organization and to know what still needs to be done. Thanks!

[kevinlibuit]

Thanks! BTW, it doesn't look like I have the capabilities of deleting this issue.

[kthyng]

eh ok, let's just leave it as is.