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!! 🔥

@alexjprobst.bsky.social look at this, we’re drilling over here!! 🥳

I don’t trust the metaspades flag. The workflow Meren linked below would work to. If you need other/our scripts, email me

either use anvio or send me an email and we can share our scripts to find circular contigs from sam files.

Depends on the length of the contigs.
for long contigs, you need to find paired reads where one of them maps at one end and the other at the other end. You should have multiple read pairs fulfilling that criterion.
Yet, it’s way more complicated if the contigs are short!

If you wanna take over my job for a few months, by all means 🤣🤣🤣

indeed!!!!

Links: Grafik einer DNA-Helix vor einem weiß/roten Binärcode. Rechts daneben steht die Überschrift des im Post verlinkten Artikels: „Daten mit Erkennungsmarke“. Es folgt dessen Vorspann mit dem Text: " In die Erhebung öffentlich zugänglicher Sequenzdaten ist oft viel Zeit und Geld geflossen. Das sollte besser gewürdigt werden, findet ein Konsortium aus der Mikrobiologie“…

Daten sind zum Teilen da: Alexander Probst von der Universität Duisburg-Essen und Kolleg:innen haben ein Konzept für die faire Nachnutzung öffentlicher Mikrobiom-Sequenzdaten entwickelt. Larissa Tetsch hat mehr dazu 👉 www.laborjournal.de/editorials/3...
@alexjprobst.bsky.social @unidue.bsky.social

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Our own @alexjprobst.bsky.social @geomicrosoares.bsky.social and Cristina Moraru have recently authored a @natmicrobiol.nature.com Consensus Statement where they discuss new mechanisms for sequencing data reuse! 🧬💻

Check out their manuscript here:
www.nature.com/articles/s41...

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk

New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!

Congrats, Ralf et al! :)

Diverging fish biodiversity trends in cold and warm rivers and streams - Nature In the past three decades, fish abundance, richness and uniqueness have diverged across cold and warm streams, and the effects on native fish communities of stream warming and increases in introduced fishes have magnified each other.

Exciting collaboration with colleagues from the US and Frederik de Laender - lead by S. Rumschlag and Mike Mahon - on how climate change has lead to alterations in US fish diversity over the last decades. Paper just out: www.nature.com/articles/s41...

it was a pleasure, Gary!

Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, inc...

New paper alert with @alexjprobst.bsky.social.

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

cool paper, congrats!
have you considered naming it under the @seqcode.bsky.social instead of calling it a Candidatus which has no priority?

Genomic and physiological characterization of 'Candidatus Methylocystis sumavensis', a novel acid-tolerant methanotroph from peatland Methanotrophic bacteria in peatlands mitigate emissions of methane (CH4), a potent greenhouse gas. Yet, the identity, physiology, and adaptive traits of methanotrophs inhabiting acidic peatlands are s...

📢 🦠 A new methanotroph from Czech peat! Through an effort led by PhD student in my group Justus Nweze we isolated and describe a new CH4-muncher. Potential for a flexible (annaerobic) metabolisms and cool pH adaptations.

www.biorxiv.org/content/10.1...
#microbesky #microbiomesky

Mein Beileid, liebe Sigrid. Fühl dich gedrückt.

I also got only one spot here… they are really rare unfortunately…

did you buy them or „hunt“ them? ;)

Congrats, Matt! Can‘t wait to see your latest results! Hopefully some new cool tools :)

The Central Collection of Algal Cultures (CCAC) at @unidue.bsky.social is advertising a 3-year PhD position supervised by the current Curator, Dr. Olga Matantseva!
This PhD will take place in close collaboration with the @jgi.doe.gov. 🦠🧬💻
Apply here: www.uni-due.de/karriere/ste...

A diverse and distinct microbiome inside living trees - Nature Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...

#NatMicroPicks

Hidden microbial world in trees🌳

Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.

#PlantMicro #MicroSky

www.nature.com/articles/s41...

Uranium mining fuels evolution in deep groundwater microbiomes Microbial communities in the deep biosphere underpin global biogeochemical cycles, yet their evolutionary responses to extensive anthropogenic disturbances remain unclear. Uranium in-situ leaching (IS...

Fresh out of the oven! 🍞
We're happy to see this preprint out, fruit of a recent collaboration with @wei-biogeochem.bsky.social! 🧬💻

Small 🧵 below going through the main points 👇
www.biorxiv.org/content/10.1...

We once collaborated with another lab by analyzing metagenomes (create MAGs, analyze the metabol. etc). The PI asked me for a conversation during which he explained to me that the work we do is technical & no real contribution. He does not consider bioinformatics science. Never worked w/ him again.

There exist some metrics that do not consider multi-author papers even though someone is corresponding/first/last author. Itms these metrics that probably make people reduce the number of authors. Yet, I think this is bs & as long as someone has made a genuine contribution they should be an author.

Retraction The Research Article “A bacterium that can grow by using arsenic instead of phosphorus” by F. Wolfe-Simon et al. (1) has been the subject of discussion and critique since its online publication in 201...

15 years later, finally, Science did the right thing at retracted the As life disaster paper! www.science.org/doi/10.1126/...

Take a photo with your iphone and you can copy from the photo!
(it’s a 16S rRNA seq of an uncultivated archaeon)

For more information about the MEB team and the position, please visit:
www.uni-due.de/umb/enzym_ho...