Thread by @rrwick

New paper for the new year! It compares different long-read assemblers for microbial genome assembly:
f1000research.com/articles/8-213…

Two Twitter threads follow - one about the paper itself and one about my experience with @F1000Research.
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In this paper, we did a ton of long-read microbial genome assemblies (using both real and simulated long-read sets) to see how the current assemblers perform.
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I won't get into detailed results here, but very briefly: Flye, Raven and Miniasm/Minipolish were our favourites, each excelling in particular ways 🏆
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Now for the exciting part: this paper will be a living document! I.e. as new versions or new assemblers are released, we will run our tests again and update the paper.
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I hope this will make this paper relevant for a longer period of time. And I hope a bit of friendly competition helps spur continued development of the assemblers 😀
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@F1000Research This was my first paper with @F1000Research, and the whole process was very positive! They were incredibly responsive, e.g. they did the initial round of copy edits less than 24 hours after we submitted.
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It was also my first experience with @overleaf, which F1000Research uses for LaTeX-formatted papers. I'm not great with LaTeX, but Overleaf was pretty easy to use.
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F1000Research were very keen to work with us on the whole living document format - allowing for new versions of the paper to come out with updated results. Very grateful that they are willing to be trailblazers in this regard.
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I also like that they host the entire article's lifespan, both pre- and post-peer review. It meant I didn't have to manage two different formats (the bioRxiv version and the journal version) like I have with previous papers.
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There's still plenty left to do (including the entire peer review process), but so far I'm a big fan of F1000Research. Thanks to everyone there for their great work!
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