Starter pack for metagenomics and microbial genomics lovers.
go.bsky.app/MFipoLH
go.bsky.app/MFipoLH
November 15, 2024 at 2:51 AM
Starter pack for metagenomics and microbial genomics lovers.
go.bsky.app/MFipoLH
go.bsky.app/MFipoLH
CoverM is published!
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics
AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r
academic.oup.com
April 9, 2025 at 1:24 PM
CoverM is published!
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
Interested in eukaryotic algal evolution, metagenomics, new plastid diversity, and more? Check out my poster (P175) today at #eseb2025 ! #protistsonsky
August 21, 2025 at 8:50 AM
Interested in eukaryotic algal evolution, metagenomics, new plastid diversity, and more? Check out my poster (P175) today at #eseb2025 ! #protistsonsky
A genomic test is the optimal way to rapidly diagnose central nervous system infections, 7-year performance data in thousands of patients
for metagenomics next-gen sequencing
www.nature.com/articles/s41...
for metagenomics next-gen sequencing
www.nature.com/articles/s41...
https://nature.com/articles/s4159…
November 12, 2024 at 2:54 PM
A genomic test is the optimal way to rapidly diagnose central nervous system infections, 7-year performance data in thousands of patients
for metagenomics next-gen sequencing
www.nature.com/articles/s41...
for metagenomics next-gen sequencing
www.nature.com/articles/s41...
New preprint: we sequenced one soil sample with ultra-deep hybrid metagenomics and found…
→ 800+ MAGs
→ 11,000+ BGCs
→ and still nowhere near saturation.
Soil is wild.
Preprint here: www.biorxiv.org/content/10.1...
#microbiome #metagenomics #BGCs #naturalproducts #secmet
→ 800+ MAGs
→ 11,000+ BGCs
→ and still nowhere near saturation.
Soil is wild.
Preprint here: www.biorxiv.org/content/10.1...
#microbiome #metagenomics #BGCs #naturalproducts #secmet
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes
Background Soil ecosystems have long been recognized as hotspots of microbial diversity, but most estimates of their complexity remain speculative, relying on limited data and extrapolation from shall...
www.biorxiv.org
May 30, 2025 at 1:47 PM
New preprint: we sequenced one soil sample with ultra-deep hybrid metagenomics and found…
→ 800+ MAGs
→ 11,000+ BGCs
→ and still nowhere near saturation.
Soil is wild.
Preprint here: www.biorxiv.org/content/10.1...
#microbiome #metagenomics #BGCs #naturalproducts #secmet
→ 800+ MAGs
→ 11,000+ BGCs
→ and still nowhere near saturation.
Soil is wild.
Preprint here: www.biorxiv.org/content/10.1...
#microbiome #metagenomics #BGCs #naturalproducts #secmet
8/Lab response is now multilayered:
🔬 PCR confirmation — South Africa's NICD
🔬 Additional samples → Institut Pasteur, Dakar
🧬 Full genome sequencing + metagenomics running
Metagenomics casts a wide net, it can detect anything in a sample, not just what you're looking for.
🔬 PCR confirmation — South Africa's NICD
🔬 Additional samples → Institut Pasteur, Dakar
🧬 Full genome sequencing + metagenomics running
Metagenomics casts a wide net, it can detect anything in a sample, not just what you're looking for.
May 5, 2026 at 12:08 PM
8/Lab response is now multilayered:
🔬 PCR confirmation — South Africa's NICD
🔬 Additional samples → Institut Pasteur, Dakar
🧬 Full genome sequencing + metagenomics running
Metagenomics casts a wide net, it can detect anything in a sample, not just what you're looking for.
🔬 PCR confirmation — South Africa's NICD
🔬 Additional samples → Institut Pasteur, Dakar
🧬 Full genome sequencing + metagenomics running
Metagenomics casts a wide net, it can detect anything in a sample, not just what you're looking for.
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology
PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.
www.nature.com
February 4, 2026 at 8:20 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Great paper by @target-amr.bsky.social leadership team colleagues @drtessjohnson.bsky.social and Steph Johnson on the ethics of clinical metagenomics
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Clinical metagenomics: ethical issues
Metagenomics is increasingly used for diagnosis in hospital settings. It is useful particularly in cases of unknown aetiology, where novel or difficult-to-diagnose pathogens are suspected, and/or foll...
www.microbiologyresearch.org
May 9, 2025 at 8:35 AM
Great paper by @target-amr.bsky.social leadership team colleagues @drtessjohnson.bsky.social and Steph Johnson on the ethics of clinical metagenomics
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Useful benchmarking study
'Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection'
www.nature.com/articles/s41...
'Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection'
www.nature.com/articles/s41...
Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection - Scientific Reports
Scientific Reports - Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection
www.nature.com
November 28, 2024 at 9:48 PM
Useful benchmarking study
'Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection'
www.nature.com/articles/s41...
'Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection'
www.nature.com/articles/s41...
Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42...
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
Metagenomic estimation of dietary intake from human stool - Nature Metabolism
Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.
www.nature.com
February 18, 2025 at 11:02 AM
Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42...
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
16S metagenomics
It’s 16S *amplicon* sequencing or its metagenomics. It can’t be both at the same time (although you can do hour on the same sample.)
It’s neither precise nor accurate.
It’s 16S *amplicon* sequencing or its metagenomics. It can’t be both at the same time (although you can do hour on the same sample.)
It’s neither precise nor accurate.
If you could fix one☝🏻 piece of terminology in your field, what would it be?
I’ll go first👇🏻(replying to myself like it’s normal)
I’ll go first👇🏻(replying to myself like it’s normal)
December 9, 2024 at 9:14 PM
16S metagenomics
It’s 16S *amplicon* sequencing or its metagenomics. It can’t be both at the same time (although you can do hour on the same sample.)
It’s neither precise nor accurate.
It’s 16S *amplicon* sequencing or its metagenomics. It can’t be both at the same time (although you can do hour on the same sample.)
It’s neither precise nor accurate.
#stamps2025
Metagenomics intro I: sampling & presence/absence
II: bioinformatics techniques for measuring genomes in metagenomes
III: reference-based metagenome interpretation & enhancing reference catalogs
IV: comprehensive metagenome content analysis and the challenge of bacterial strains
Metagenomics intro I: sampling & presence/absence
II: bioinformatics techniques for measuring genomes in metagenomes
III: reference-based metagenome interpretation & enhancing reference catalogs
IV: comprehensive metagenome content analysis and the challenge of bacterial strains
STAMPS 2025 tutorials - intro to metagenomics · Issue #3734 · sourmash-bio/sourmash
Metagenomics intro I: sampling & presence/absence Metagenomics intro II: bioinformatics techniques for measuring genomes in metagenomes Metagenomics intro III: reference-based metagenome interpreta...
github.com
July 18, 2025 at 1:20 PM
#stamps2025
Metagenomics intro I: sampling & presence/absence
II: bioinformatics techniques for measuring genomes in metagenomes
III: reference-based metagenome interpretation & enhancing reference catalogs
IV: comprehensive metagenome content analysis and the challenge of bacterial strains
Metagenomics intro I: sampling & presence/absence
II: bioinformatics techniques for measuring genomes in metagenomes
III: reference-based metagenome interpretation & enhancing reference catalogs
IV: comprehensive metagenome content analysis and the challenge of bacterial strains
Delighted to share that I’ve been awarded one of just four 2026 @pacbio.bsky.social Metagenomics SMRT Grants! 🧬
The grant will support my work in the @halllab.bsky.social at @unibirmingham.bsky.social , exploring long-read #metagenomics, #AMR & #DNAmethylation 🔬👩🏼🔬
#microbialgenomics #ECR #PacBio
The grant will support my work in the @halllab.bsky.social at @unibirmingham.bsky.social , exploring long-read #metagenomics, #AMR & #DNAmethylation 🔬👩🏼🔬
#microbialgenomics #ECR #PacBio
We’re excited to announce 4 winners for the 2026 Metagenomics SMRT Grant! 🧬
From infant resistomes and hereditary cancer to soil pathogens and HPV persistence, see how these researchers are driving discovery with PacBio HiFi sequencing.
Meet the awardees: https://bit.ly/4rotusF
From infant resistomes and hereditary cancer to soil pathogens and HPV persistence, see how these researchers are driving discovery with PacBio HiFi sequencing.
Meet the awardees: https://bit.ly/4rotusF
September 22, 2026 at 7:52 PM
Delighted to share that I’ve been awarded one of just four 2026 @pacbio.bsky.social Metagenomics SMRT Grants! 🧬
The grant will support my work in the @halllab.bsky.social at @unibirmingham.bsky.social , exploring long-read #metagenomics, #AMR & #DNAmethylation 🔬👩🏼🔬
#microbialgenomics #ECR #PacBio
The grant will support my work in the @halllab.bsky.social at @unibirmingham.bsky.social , exploring long-read #metagenomics, #AMR & #DNAmethylation 🔬👩🏼🔬
#microbialgenomics #ECR #PacBio
Interested in a PhD on viral metagenomics from clinical samples? Check out this collaborative project between my group at @biology.ox.ac.uk and @eit.org
eit.org/project/viro...
eit.org/project/viro...
Virome metagenomics from clinical samples
eit.org
September 17, 2026 at 8:12 PM
Interested in a PhD on viral metagenomics from clinical samples? Check out this collaborative project between my group at @biology.ox.ac.uk and @eit.org
eit.org/project/viro...
eit.org/project/viro...
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
www.nature.com
November 26, 2025 at 9:55 PM
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Will be discussing "Genome Resolved Metagenomics" in EVE161 course at @ucdavis.bsky.social today. Using this review paper to guide discussion
Genome-resolved metagenomics: a game changer for microbiome medicine
www.nature.com/articles/s12...
Genome-resolved metagenomics: a game changer for microbiome medicine
www.nature.com/articles/s12...
Genome-resolved metagenomics: a game changer for microbiome medicine - Experimental & Molecular Medicine
The human body houses numerous microbes, tiny organisms, that are vital for our health. This research aims to overcome limitations using genome-resolved metagenomics, a method that assembles complete ...
www.nature.com
March 6, 2025 at 4:09 PM
Will be discussing "Genome Resolved Metagenomics" in EVE161 course at @ucdavis.bsky.social today. Using this review paper to guide discussion
Genome-resolved metagenomics: a game changer for microbiome medicine
www.nature.com/articles/s12...
Genome-resolved metagenomics: a game changer for microbiome medicine
www.nature.com/articles/s12...
Metagenomics, microbial genomics by @yishay.bsky.social bsky.app/starter-pack...
November 15, 2024 at 9:56 AM
Metagenomics, microbial genomics by @yishay.bsky.social bsky.app/starter-pack...
Folks - if you're interested in how machine learning/AI can be used for microbial genomics, microbiome and metagenomics studies - please join us for a workshop in Birmingham on Thursday 8th October organised with CLIMB & NVIDIA. www.climb.ac.uk/blog/2026/09...
Call for Applications: GPU-Accelerated Computing for Microbiome and Metagenomic Research · CLIMB
CLIMB is a cloud computing infrastructure for microbial bioinformatics — notebook servers, shared storage and reproducible workflows for genomics, metagenomics and pathogen surveillance researchers ac...
www.climb.ac.uk
September 22, 2026 at 2:01 PM
Folks - if you're interested in how machine learning/AI can be used for microbial genomics, microbiome and metagenomics studies - please join us for a workshop in Birmingham on Thursday 8th October organised with CLIMB & NVIDIA. www.climb.ac.uk/blog/2026/09...
Excited to introduce the preprint for CoverM: the Swiss Army knife of coverage calculators for metagenomics! 🧬🖥️ DOI: doi.org/10.48550/arX...
@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social
@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social
January 22, 2025 at 6:11 AM
Excited to introduce the preprint for CoverM: the Swiss Army knife of coverage calculators for metagenomics! 🧬🖥️ DOI: doi.org/10.48550/arX...
@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social
@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social
I’ve been maintaining a list of shotgun #metagenomics tools and resources which I got Claude to turn into a GitHub repo. It has 300+ entries.
Please share and tell me if I’ve missed anything!
github.com/feargalr/Met...
#microbiota #bioinformatics #microbiome #genomics
Please share and tell me if I’ve missed anything!
github.com/feargalr/Met...
#microbiota #bioinformatics #microbiome #genomics
GitHub - feargalr/Metagenomics-tools-atlas: An inventory of tools and resources for short-read shotgun metagenomics.
An inventory of tools and resources for short-read shotgun metagenomics. - feargalr/Metagenomics-tools-atlas
github.com
June 15, 2026 at 12:48 AM
I’ve been maintaining a list of shotgun #metagenomics tools and resources which I got Claude to turn into a GitHub repo. It has 300+ entries.
Please share and tell me if I’ve missed anything!
github.com/feargalr/Met...
#microbiota #bioinformatics #microbiome #genomics
Please share and tell me if I’ve missed anything!
github.com/feargalr/Met...
#microbiota #bioinformatics #microbiome #genomics
Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota
August 7, 2025 at 2:50 AM
Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota
Hallo Robert, hallo Berlin Metagenomics Network Symposium
September 15, 2026 at 7:11 AM
Hallo Robert, hallo Berlin Metagenomics Network Symposium
Recent microbial evolutionary insights from metagenomics academic.oup.com/gbe/advance-... #jcampubs
February 11, 2026 at 4:02 PM
Recent microbial evolutionary insights from metagenomics academic.oup.com/gbe/advance-... #jcampubs