🧪🦠🖥️🧬🧫🔬 The Roadmap for equitable use of public microbiome data -including the Data Reuse Information Tag (DRI)- by the #DataReuseConsortium.
Must read if you use or produce microbiome data!

Kudos to the Data Reuse Core Team for their hard work!

doi.org/10.1038/s415...

It's geNomad, VirSorter2, VIBRANT, ViralVerify and DeepVirusFinder. I had to write a workflow (github.com/CristinaMora...) to make the consensus from of all these outputs. The code is not ready yet to share with the world, but soon. I'm benchmarking it and your coralreef dataset drew my attention.

I believe the difference between CheckV and CheckM lies in the difference in our knowledge regarding prok and viruses. On top of beeing extremely diverse, viruses have also much more hypothetical genes, so we can't estimate the genome completeness just from looking at their genes.

I tested various values for the score and for the p-value. Finally, I settled on 0.7 for score and 0.01 for p-value. But, I used DVF in conjunction with other predictor, and that compensated for the false negatives. And I agree, there is a need for further benchmarking.

I've noticed the same with DVF and CheckV for long contigs. My way of dealing with it was to use a very high score threshold for DVF to remove non-viral contigs. Of course, shorter true viral contigs are also lost, but I'm using multiple predictors, so hopefully that compensates for their loss

I’ve written threads about the GBR-MGDs pMAGs, but it also contains viruses (vMAGs), including a monophyletic clade of marine Crassvirales, chromosome-level eukaryote eMAGs, and putative plasmids. We wanted a holistic DB.

One problem: some key software appear to break with long reads. A 🦠 🧵.

Just a reminder to please fill out this form if you’d be interest in an EVE / ERV meeting 📋🥳

We seek PhD students fascinated by aquatic 🧫🦠🪱🦟🐟 who want to unravel tolerances, dispersal patterns and biotic interactions with field studies, field experiments, metagenomics, statistical and mechanistic models.

Why come to Essen in 🇩🇪🇪🇺? Great research environment, many water-related disciplines involved, creative work atmosphere, competitive PhD salary (esp. compared to 🇺🇲🇨🇦), affordable living costs and - yes - nice people.

Become part of the @crc-resist.bsky.social as a 𝗣𝗵𝗗 student based in my lab at #UDE working on '𝗥𝗲𝘀𝗽𝗼𝗻𝘀𝗲𝘀 𝗼𝗳 𝗽𝗮𝗿𝗮𝘀𝗶𝘁𝗶𝗰 𝗽𝗿𝗼𝘁𝗶𝘀𝘁 𝗰𝗼𝗺𝗺𝘂𝗻𝗶𝘁𝗶𝗲𝘀 𝗮𝗻𝗱 𝘁𝗵𝗲𝗶𝗿 𝗲𝗳𝗳𝗲𝗰𝘁𝘀 𝗼𝗻 𝘁𝗵𝗲𝗶𝗿 𝗺𝗮𝗰𝗿𝗼𝗶𝗻𝘃𝗲𝗿𝘁𝗲𝗯𝗿𝗮𝘁𝗲 𝗵𝗼𝘀𝘁𝘀 𝘂𝗻𝗱𝗲𝗿 𝗱𝗶𝗳𝗳𝗲𝗿𝗲𝗻𝘁 𝗱𝗲𝗴𝗿𝗮𝗱𝗮𝘁𝗶𝗼𝗻 𝗮𝗻𝗱 𝗿𝗲𝗰𝗼𝘃𝗲𝗿𝘆 𝗰𝗼𝗻𝗱𝗶𝘁𝗶𝗼𝗻𝘀' 🔬 🧫 🦐 🪱 🌊

www.uni-due.de/karriere/ste...

Please share!

Wanted: microbial ecology + bioinformatics enthusiasts for 2 PhD positions (@probstlab.bsky.social)

#1 on microbial & epigenetic stress response in rivers tinyurl.com/bdf8eu5a
#2 on virus-host stress response in rivers tinyurl.com/43cjd6es

@alexjprobst.bsky.social
@unidue.bsky.social

#PhD #position #alert

2 bioinfo PhD positions @ProbstLab @RESIST_CRC
#1 on microbial & epigenetic stress response in rivers
tinyurl.com/bdf8eu5a
#2 on virus-host stress response in rivers
tinyurl.com/43cjd6es (supervision Moraru)

Please share!

@probstlab.bsky.social
@crc-resist.bsky.social

#1 on virus-host stress response in rivers tinyurl.com/43cjd6es

#2 on microbial & epigenetic stress response in rivers tinyurl.com/bdf8eu5a

@alexjprobst.bsky.social
@unidue.bsky.social

Pls RT!

dsRNA viruses from Picobirnaviridae potentially infect bacterial and not animal hosts, as suggested by the enrichment of bacterial RBS in picobirnavirus genomes:
www.biorxiv.org/content/10.1...

Ancient bacteriophages in a collection of gut and faecal samples from 150 to 5300 years ago: www.nature.com/articles/s41...

Interesting preprint, describing Obelisks - circular RNA viroid-like elements present globally in microbiomes:
www.biorxiv.org/content/10.1...

Please RT and share with other scientists (PhD students, PostDocs & Profs) that are data creators/users in #metagenomics or other #omics! Me, @lhug.bsky.social @environmicrobio.bsky.social @alexjprobst.bsky.social @cristinamoraru.bsky.social & @folker.bsky.social will appreciate all community input!