A paper on how microbiologists navigate the tension between reductionism and complexity in their everyday practices, and my 2 cents on it.
miscellaneous Mon, Dec 15, 2025
Marine Microbial Observatories for the Future - From Samples to Data to Legacy in the Era of Integrated ‘Omics
miscellaneous Mon, Nov 17, 2025
A means for ECRs to get advice from a senior scientist outside of their support network
miscellaneous Sun, Nov 16, 2025
Meren's pilgrimage to Barhal
miscellaneous Mon, Sep 01, 2025
A thought in structures that helps us become who we want to become
miscellaneous Wed, Jul 16, 2025
Matt's first time sampling water from a CTD
miscellaneous Sat, Apr 08, 2023
A journey into the genomics of giant viruses and their close relatives
miscellaneous Mon, Jan 03, 2022
Using metabolism estimation to go fishing in some ocean metagenomes.
miscellaneous Wed, Oct 20, 2021
Or, Meren's personal notes from a 48 hours, high-resolution, diel sampling effort in Hawai'i.
miscellaneous Mon, Sep 13, 2021
An attempt to learn from the experiences of ECRs with their mentors
miscellaneous Tue, Jun 01, 2021
miscellaneous Mon, Oct 05, 2020
A personal and directed look at the past of an exciting discipline.
miscellaneous Mon, Jul 27, 2020
A blog post detailing InteracDome's integration into anvi'o
anvio Wed, Jul 22, 2020
On how we unified the known and unknown CDS-space in genomes and metagenomes
miscellaneous Wed, Jul 01, 2020
Socially isolated community discussions on key concepts and stuff.
miscellaneous Sat, Jun 27, 2020
Don't click. Run away. Don't see what you don't want to see.
miscellaneous Thu, Jan 02, 2020
Inflating the number of near-identical genomes versus losing potentially key genetic information in genome-resolved metagenomics studies.
miscellaneous Thu, Dec 12, 2019
Ways to visualize mapping results in anvi'o to make informed statements about environmental populations and to generate high-quality figures)
anvio Mon, Nov 25, 2019
A flexible and scalable approach to locate and extract target genetic loci from larger genetic contexts.
anvio Thu, Oct 17, 2019
An attempt at alchemy combining the magic of GTDB and single-copy core genes in anvi'o.
anvio Tue, Oct 08, 2019
A primer on how to find your way through the maze of microbial 'omics and anvi'o
anvio Mon, Oct 07, 2019
How to download, process, and combine genomes from NCBI in your phylogenomic, pangenomic, and/or other 'omics analyses
anvio Thu, Mar 14, 2019
After 24 months of work, our study describing the discovery of a plasmid for Wolbachia appeared in Nature Communications. I thought that this would be a good moment to take a break and think through everything that led to this proud moment and learn from it.
miscellaneous Tue, Mar 05, 2019
A small checklist for reviewers to follow to make public data sources public and forever
miscellaneous Sun, Feb 24, 2019
One of those 'I can not believe you are even considering reading this' posts
miscellaneous Mon, Dec 17, 2018
Mike Lee heroically combines reference annotations with new annotations
anvio Sat, Dec 01, 2018
A light introduction to questions of microbial ecology and microbial omics through the story of crassphage
anvio Sun, Sep 09, 2018
A discussion on the practical and theoretical aspects of using anvi'o structure
anvio Tue, Sep 04, 2018
Bringing the magic of anvi'o together with the wonders of snakemake.
anvio Mon, Jul 09, 2018
A preliminary set of 83 HMMs from BUSCO. -Lol is anvi'o doing picoeuks now fam? -Why yes, yes it does.
anvio Sat, May 05, 2018
A hacker's guide to anvi'o networking. Are you scared? You should be!
anvio Wed, Mar 07, 2018
Details of a beautiful algorithm.
anvio Tue, Feb 13, 2018
Anvi'o projects meet the underappreciated owners of this planet.
anvio Thu, Feb 08, 2018
We just started playing with this, we have no idea what we are doing. Kthxbye.
miscellaneous Thu, Jan 18, 2018
KEGG modules, meet anvi'o. Anvi'o, meet KEGG modules.
anvio Wed, Jan 17, 2018
Getting additional data in an out of pan and profile databases like a pro.
anvio Mon, Dec 11, 2017
Dotting i's and crossing t's with this Deepwater Horizon oil plume drama.
miscellaneous Sat, Nov 25, 2017
Continuing to investigate how good that simulation was to simulate the oil spill. With a killer poem.
miscellaneous Mon, Oct 16, 2017
And a realization of my own unintentional conformism that is part of a bigger problem
miscellaneous Thu, Sep 14, 2017
Astonishing if its true. Astonishing if its false. Astonishments all over.
miscellaneous Wed, Aug 23, 2017
Use anvi'o to get rRNA genes out of single-cells, clultivars, metagenome-assembled genomes, or even from entire metagenomic assemblies because why not.
anvio Sun, Jul 09, 2017
It may sound cool today, but it will likely be a bit embarrassing to look back and see it in our history in about two decades from now.
miscellaneous Thu, Jun 22, 2017
On a journey characterizing a thousand population genomes from the surface of oceans and seas
miscellaneous Sun, May 21, 2017
If Prokka doesn't come to you, you go to Prokka
anvio Thu, May 18, 2017
Just for you. Well, also for others. And totally free! Except you pay for your travel. But then it may be a lot of fun. MAYBE.
miscellaneous Wed, May 17, 2017
Is the big brother watching you? If he does, what does he see?
anvio Tue, May 16, 2017
More than just completion and redundancy estimates
anvio Thu, May 11, 2017
Just for you. Well, also for others. And totally free! Except you pay for your travel. But then it may be a lot of fun. MAYBE.
miscellaneous Thu, Mar 23, 2017
Has decades of suffering of thousands of anvi'o users come to an end?
anvio Tue, Mar 07, 2017
From the paper 'Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica'
miscellaneous Sun, Feb 05, 2017
Curating the composite metagenome-assembled genome Lokiarchaeum sp. GC14_75 with anvi'o
miscellaneous Tue, Jan 03, 2017
The way we made sure everyone has access to the genomes we recovered
miscellaneous Mon, Nov 21, 2016
The user-friendly interface anvi'o provides to work with pangenomes.
anvio Tue, Nov 08, 2016
In other words, not putting screenshots in papers
anvio Thu, Oct 27, 2016
Yes. Good ol' COGs. Into your contigs db. Just like that. 60% of the time, every time.
anvio Tue, Oct 25, 2016
A resource to find out whether we are coming to or you just missed an event close to a location near you.
anvio Thu, Aug 18, 2016
A tale from 4,000+ gold standard bacterial genomes to justify 'max 10% redundancy'
miscellaneous Thu, Jun 09, 2016
A prestigious post-doc opportunity at a great university environment
miscellaneous Wed, Jun 08, 2016
So you have an assembly, or a draft genome, or a MAG, but no metagenomic short reads? That's OK.
anvio Mon, Jun 06, 2016
Mike Lee demonstrates how to use a custom HMM single-copy gene profile for archaeal genomes
anvio Sat, May 21, 2016
A second look at the genomes published by Brown CT. et al
miscellaneous Sun, Apr 17, 2016
Musings from my recent visits to Berkeley, Stanford, USC, and SDSU
miscellaneous Fri, Apr 08, 2016
Data types, usage tips, and other stuff about the interface
anvio Sat, Feb 27, 2016
Musings over a *Nitrospira* genome that can do complete nitrification
anvio Wed, Dec 09, 2015
A quick way to get an insight into the number of genomes your contigs represent.
anvio Mon, Dec 07, 2015
For people who does not have time to download stuff.
anvio Sat, Nov 28, 2015
The user-friendly interface anvi'o provides to work with pangenomes.
anvio Sat, Nov 14, 2015
Do you want to try anvi'o? Do you have a MAC computer? We got you covered.
anvio Thu, Aug 20, 2015
Exploring micro-diversity patterns using for deeper insights into ecology
anvio Mon, Jul 20, 2015
Anvi'o provides an interface to screen for possible contaminants and curate individual genomes
anvio Thu, Jun 25, 2015
Bowtie, Bowtie2, BWA, CLC, GSNAP, BBMap, Novoalign, and SMALT.
anvio Tue, Jun 23, 2015
Tricks for people who like to go deeper.
anvio Wed, Jun 10, 2015
Life at the extremes: microbial EcoGenomics of deep-sea extremophiles
miscellaneous Fri, May 22, 2015
Dealing with heavily contaminated bins identified in an unsupervised manner.
anvio Mon, May 11, 2015
A small-scale meeting to make a statement about high-resolution.
oligotyping Sat, Mar 14, 2015
A summary of the oligotyping special topic in Frontiers In Microbiology
oligotyping Thu, Feb 12, 2015
1nt resolution at marker gene analyses!
Tue, Nov 04, 2014
Answers to some of the questions that have been asked frequently
oligotyping Sun, Sep 14, 2014
For people who does not want to install the pipeline
oligotyping Tue, Sep 02, 2014
Installing the pipeline shall not be a PITA.
oligotyping Sat, Aug 16, 2014
In which we oligotyped the entire oral microbiome data generated by the HMP...
oligotyping Wed, Jun 25, 2014
A special topic for oligotyping
oligotyping Thu, Dec 12, 2013
It is published in Methods in Ecology and Evolution...
oligotyping Wed, Oct 16, 2013
The oligotyping pipline generates Gephi-compatible network descriptions.
oligotyping Fri, Mar 29, 2013
A study that shows the connection between human microbiome and the sewage
oligotyping Thu, Feb 28, 2013
If you have a categorical mapping file, the oligotyping pipeline can deliver more
oligotyping Mon, Feb 04, 2013
How to install, and how to start using the oligotyping pipeline
oligotyping Fri, May 11, 2012
The first story we recovered using oligotyping
oligotyping Wed, May 02, 2012