Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
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github.com/bluenote-157...
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
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
Nature research paper: Long-read metagenomics reveals phage dynamics in the human gut microbiome
go.nature.com/44zgo1o
Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv.
Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen)
github.com/bluenote-157...
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Excited to share our review relating to the giant extrachromosomal elements (ECEs)
We cover: why long-read metagenomics enables their discovery, genomic comparisons across recently characterized examples, and limitations of current classification tools.
www.cell.com/trends/genet...
Jim Shaw
Our review on the Japanese gut microbiome is now published!
By analyzing >30,000 gut metagenomes from 37 countries🧬, we re-evaluated the unique feature of the Japanese gut microbiome🦠 in a global context🌏.
doi.org/10.2183/pjab...
Mushuvirus is the most widespread phage genus in the human gut. 🌍
Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi!
How is it possible that they were hidden in previous metagenomic analyses?
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Read: doi.org/10.64898/202...
Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social.
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
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–bacterial interactions in the human gut microbiome.
Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are
intracellular replicons maintained independently of the primary chromosome. Historically,
the ECE research field ha...
Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in t …
Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
