Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
go.nature.com
January 2, 2026 at 4:39 PM
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Troubleshooting common errors in assemblies of long-read metagenomes www.nature.com/articles/s41... #jcampubs
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
www.nature.com
January 2, 2026 at 8:30 PM
Troubleshooting common errors in assemblies of long-read metagenomes www.nature.com/articles/s41... #jcampubs
Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
January 6, 2026 at 9:38 AM
Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
An incredible resource: >8000 bat virus metagenomes ... www.nature.com/articles/s41...
A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics - Nature Microbiology
Samples from over 4,000 bats representing 40 different species yield 8,176 viral metagenomes that expand RNA virus diversity and decipher environmental and anthropogenic factors influencing bat viral ...
www.nature.com
January 22, 2025 at 5:13 PM
An incredible resource: >8000 bat virus metagenomes ... www.nature.com/articles/s41...
Well, this is a big data set www.nature.com/articles/s41...
Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes - Scientific Data
Scientific Data - Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes
www.nature.com
January 30, 2025 at 3:29 AM
Well, this is a big data set www.nature.com/articles/s41...
Do you like coastal/estuarine microbiology, time-series data, and/or metagenomics? Have we got a dataset for you #NSFfunded
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series - Scientific Data
Scientific Data - Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series
www.nature.com
August 11, 2025 at 4:37 PM
Do you like coastal/estuarine microbiology, time-series data, and/or metagenomics? Have we got a dataset for you #NSFfunded
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Really important read for people working with long-read MAGs.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
www.nature.com
January 6, 2026 at 6:05 AM
Really important read for people working with long-read MAGs.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
High-quality phage assembly from metagenomes with PALACE www.nature.com/articles/s41...
High-quality phage assembly from metagenomes with PALACE - Nature Biotechnology
PALACE combines homology features and deep learning to improve phage assembly from metagenomics.
www.nature.com
July 9, 2026 at 7:07 PM
High-quality phage assembly from metagenomes with PALACE www.nature.com/articles/s41...
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Assemblies of long-read metagenomes suffer from diverse errors
Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
www.biorxiv.org
April 28, 2025 at 8:08 AM
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Looking for a tool to estimate abundances of aerobes versus anaerobes directly from metagenomes? Here you go: www.biorxiv.org/content/10.6...
www.biorxiv.org
January 26, 2026 at 10:05 PM
Looking for a tool to estimate abundances of aerobes versus anaerobes directly from metagenomes? Here you go: www.biorxiv.org/content/10.6...
Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes www.nature.com/articles/s41... #jcampubs
Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes - Scientific Data
Scientific Data - Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes
www.nature.com
January 27, 2025 at 1:31 AM
Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes www.nature.com/articles/s41... #jcampubs
The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4
rdcu.be/eCbj4
Rapid species-level metagenome profiling and containment estimation with sylph - Nature Biotechnology
The microbial composition of metagenomes is identified in seconds by profiling against large databases.
go.nature.com
August 27, 2025 at 1:14 AM
The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4
rdcu.be/eCbj4
Assemblies of long-read metagenomes suffer from diverse errors https://www.biorxiv.org/content/10.1101/2025.04.22.649783v1
April 25, 2025 at 12:46 AM
Assemblies of long-read metagenomes suffer from diverse errors https://www.biorxiv.org/content/10.1101/2025.04.22.649783v1
Assemblies of long-read metagenomes suffer from diverse errors www.biorxiv.org/content/10.1... #jcampubs
April 25, 2025 at 3:19 PM
Assemblies of long-read metagenomes suffer from diverse errors www.biorxiv.org/content/10.1... #jcampubs
Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla.
doi.org/10.1101/2024...
@wwood @rhysnewell @CMR_QUT
🧵1/6
doi.org/10.1101/2024...
@wwood @rhysnewell @CMR_QUT
🧵1/6
November 26, 2024 at 2:45 AM
Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla.
doi.org/10.1101/2024...
@wwood @rhysnewell @CMR_QUT
🧵1/6
doi.org/10.1101/2024...
@wwood @rhysnewell @CMR_QUT
🧵1/6
🦠🧫🖥🧬🧪🔬
Every metagenomic paper without experimental design:
Every metagenomic paper without experimental design:
March 25, 2025 at 1:14 PM
🦠🧫🖥🧬🧪🔬
Every metagenomic paper without experimental design:
Every metagenomic paper without experimental design:
Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models www.biorxiv.org/content/10.6... #jcampubs
April 11, 2026 at 11:25 PM
Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models www.biorxiv.org/content/10.6... #jcampubs
Genomes from long-read metagenomic assemblies contain rampant errors, highlighting the pressing need for stricter evaluation methods in long-read assembly algorithms. Read more in our paper with the Eren group. @floriantrigodet.bsky.social @merenbey.bsky.social
April 28, 2025 at 9:29 PM
Genomes from long-read metagenomic assemblies contain rampant errors, highlighting the pressing need for stricter evaluation methods in long-read assembly algorithms. Read more in our paper with the Eren group. @floriantrigodet.bsky.social @merenbey.bsky.social
Our data descriptor that includes surface ocean metagenomes (with Illumina & PacBio), metatranscriptomes, and tRNAs transcripts from Hawaiʻi is now out:
www.nature.com/articles/s41...
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
www.nature.com/articles/s41...
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts - Scientific Data
Scientific Data - A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts
www.nature.com
December 5, 2025 at 9:03 AM
Our data descriptor that includes surface ocean metagenomes (with Illumina & PacBio), metatranscriptomes, and tRNAs transcripts from Hawaiʻi is now out:
www.nature.com/articles/s41...
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
www.nature.com/articles/s41...
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...
doi.org
June 13, 2025 at 8:22 PM
New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...
New paper out on which I am a co author on studies of metagenomes from Tramway Ridge in Antarctica phylogenomics.me/2024/12/19/n...
New paper out from studies of metagenomes from Tramway Ridge in Antarctica
I am a co-author on a new paper that just came out. Nutritional niches of potentially endemic, facultatively anaerobic heterotrophs from an isolated Antarctic terrestrial hydrothermal refugium eluc…
phylogenomics.me
December 19, 2024 at 6:50 PM
New paper out on which I am a co author on studies of metagenomes from Tramway Ridge in Antarctica phylogenomics.me/2024/12/19/n...
New pre-print alert! 🚨🫁
COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9
www.biorxiv.org/content/10.1...
COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9
www.biorxiv.org/content/10.1...
www.biorxiv.org
June 17, 2025 at 7:47 AM
New pre-print alert! 🚨🫁
COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9
www.biorxiv.org/content/10.1...
COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9
www.biorxiv.org/content/10.1...
The new version of MetaPhlAn v4.2.2 released!
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)
Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...
forum.biobakery.org
June 11, 2025 at 6:15 AM
The new version of MetaPhlAn v4.2.2 released!
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
The gut microbiome uniqueness increases with age but is not associated with longevity or changed ("rejuvenated") by caloric restriction @natmicrobiol.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Microbiome ageing in genetically diverse mice - Nature Microbiology
A dataset of 2,997 metagenomes from 913 genetically diverse mice provides insights into microbiome interactions with ageing, dietary restriction, host genetics and longevity.
www.nature.com
May 7, 2025 at 12:13 PM
The gut microbiome uniqueness increases with age but is not associated with longevity or changed ("rejuvenated") by caloric restriction @natmicrobiol.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com/articles/s41...