“first drafts of Results, Discussion, and Introduction should be the trainee’s own work. AI can help with grammar…tightening prose…critiquing the logic of an argument you’ve already made. But the hard part of forming the argument needs to be yours.’ blekhman.substack.com/p/you-need-t...
Figure 1 shows the conceptual workflow of the algorithm. It first loads the configuration file and the input data of one or multiple binned metagenomes, yet evaluates each bin individually. It then iteratively processes each candidate bin in the input, going through the refinement tasks, potentially multiple times. The refinement either stops when the last step or a preset stop task have been reached or an unrecoverable error has been encountered. The algorithm tasks can be configured individually.
🤯 Manual MAG refinement? Still doing it by hand??
We’ve been there... You could just leave those messy, ill-assigned contigs/scaffolds in your data for NCBI to pick up during your submission…
…OR you could add itBins, our new automated MAG refiner by @jmk-ude.bsky.social, to your pipeline!! 🔥
Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.
rdcu.be/famFj
Many journals require data and code sharing. Yet code is still rarely shared and datasets are often hard to reuse.
Our new paper introduces the @sortee.bsky.social guidelines for data & code quality control in ecology & evolution, developed by 26 experienced data editors.
📄 doi.org/10.24072/pcj...
Scihub stopped uploading new articles. SciDB is a continuing effort which has the entire scihub collection AND new papers.
annas-archive.org/scidb
HMMER is the bedrock of genomic annotation globally, and now its funding is terminated for no reason.
@cryptogenomicon.bsky.social is now on bsky:
Our group photo ❤️. Big thanks to all participants for their contributions.
" (...) it is very hard to interpret big data in ecology in meaningful ways if you do not know anything about who the organisms are and what they do in the environment."
(Jennifer Powers, A place for natural history in the 21st century, Biotropica. 2025;57:e13364. doi.org/10.1111/btp....)
I am guilty of this 😅
Are most 16S primers (I use 515-926) able to capture archaeal diversity? I, for no good reason, thought they were not
