The Next 50 Years of Ocean 'Omics: Reflections from MMOFF 2025
Marine Microbial Observatories for the Future - From Samples to Data to Legacy in the Era of Integrated ‘Omics
miscellaneous Mon, Nov 17, 2025
ECR connection: Meet Meren when you need to
A means for ECRs to get advice from a senior scientist outside of their support network
miscellaneous Sun, Nov 16, 2025
The Weight of a Honey Pot: Memory, Belonging, and the Passage of Time
Meren's pilgrimage to Barhal
miscellaneous Mon, Sep 01, 2025
We do not choose our families but we can choose people who push us
A thought in structures that helps us become who we want to become
miscellaneous Wed, Jul 16, 2025
Research week at BIOS: Getting my hands wet with data
Matt's first time sampling water from a CTD
miscellaneous Sat, Apr 08, 2023
Binning giant viruses and their close relatives with anvi'o
A journey into the genomics of giant viruses and their close relatives
miscellaneous Mon, Jan 03, 2022
Targeted binning of a novel nitrogen-fixing population from the Arctic Ocean
Using metabolism estimation to go fishing in some ocean metagenomes.
miscellaneous Wed, Oct 20, 2021
From Boats to Bits: Evolution of a study on marine microbes
Or, Meren's personal notes from a 48 hours, high-resolution, diel sampling effort in Hawai'i.
miscellaneous Mon, Sep 13, 2021
Mentorship in life sciences: voices of mentees
An attempt to learn from the experiences of ECRs with their mentors
miscellaneous Tue, Jun 01, 2021
A reading list for scientists to recognize and confront anti-Black racism
miscellaneous Mon, Oct 05, 2020
The history of metagenomics: An incomplete summary
A personal and directed look at the past of an exciting discipline.
miscellaneous Mon, Jul 27, 2020
Estimating per-residue binding frequencies with InteracDome
A blog post detailing InteracDome's integration into anvi'o
anvio Wed, Jul 22, 2020
Welcome to the dark side of genomes and metagenomes
On how we unified the known and unknown CDS-space in genomes and metagenomes
miscellaneous Wed, Jul 01, 2020
Online seminar series on Microbial 'Omics for beginners
Socially isolated community discussions on key concepts and stuff.
miscellaneous Sat, Jun 27, 2020
Visualizing the fate of contigs across metagenomic binning algorithms
Don't click. Run away. Don't see what you don't want to see.
miscellaneous Thu, Jan 02, 2020
To dereplicate or not to dereplicate?
Inflating the number of near-identical genomes versus losing potentially key genetic information in genome-resolved metagenomics studies.
miscellaneous Thu, Dec 12, 2019
Visualizing contig coverages to better understand microbial population structures
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
Extract loci from genomes and metagenomes with anvi'o
A flexible and scalable approach to locate and extract target genetic loci from larger genetic contexts.
anvio Thu, Oct 17, 2019
Genome / metagenome / MAG taxonomy with anvi'o
An attempt at alchemy combining the magic of GTDB and single-copy core genes in anvi'o.
anvio Tue, Oct 08, 2019
Getting help from the anvi'o community
A primer on how to find your way through the maze of microbial 'omics and anvi'o
anvio Mon, Oct 07, 2019
Accessing and including NCBI genomes in 'omics analyses in anvi'o
How to download, process, and combine genomes from NCBI in your phylogenomic, pangenomic, and/or other 'omics analyses
anvio Thu, Mar 14, 2019
An interdisciplinary Wolbachia story through connections across the Atlantic: Metagenomics, long-read sequencing, and other things
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
Fantastic Data and How to Share Them: A Plea to Journal Editors and Reviewers
A small checklist for reviewers to follow to make public data sources public and forever
miscellaneous Sun, Feb 24, 2019
My unpopular two cents on the 'Face on a Turd'
One of those 'I can not believe you are even considering reading this' posts
miscellaneous Mon, Dec 17, 2018
Combining reference genome annotations with your own in pangenomes
Mike Lee heroically combines reference annotations with new annotations
anvio Sat, Dec 01, 2018
Microbial 'Omics Workshop
A light introduction to questions of microbial ecology and microbial omics through the story of crassphage
anvio Sun, Sep 09, 2018
Integrating sequence variants and predicted protein structures
A discussion on the practical and theoretical aspects of using anvi'o structure
anvio Tue, Sep 04, 2018
Anvi'o snakemake workflows
Bringing the magic of anvi'o together with the wonders of snakemake.
anvio Mon, Jul 09, 2018
Assessing the completion of eukaryotic bins with anvi'o
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
Running remote anvi'o interactive interfaces on your local computer
A hacker's guide to anvi'o networking. Are you scared? You should be!
anvio Wed, Mar 07, 2018
Amino acid color coding by conservation in anvi'o gene clusters
Details of a beautiful algorithm.
anvio Tue, Feb 13, 2018
Importing VirSorter annotations into anvi'o to study phages
Anvi'o projects meet the underappreciated owners of this planet.
anvio Thu, Feb 08, 2018
Getting ribosomal RNA gene sequences from a MinION run
We just started playing with this, we have no idea what we are doing. Kthxbye.
miscellaneous Thu, Jan 18, 2018
Importing GhostKOALA/KEGG annotations into anvi'o
KEGG modules, meet anvi'o. Anvi'o, meet KEGG modules.
anvio Wed, Jan 17, 2018
Working with anvi'o additional data tables
Getting additional data in an out of pan and profile databases like a pro.
anvio Mon, Dec 11, 2017
DWH O. desum v2: Most abundant Oceanospirillaceae population in the Deepwater Horizon Oil Plume
Dotting i's and crossing t's with this Deepwater Horizon oil plume drama.
miscellaneous Sat, Nov 25, 2017
Ca. Bermanella macondoprimitus is not a strain variant of the oil plume (Reply to Probst et al.)
Continuing to investigate how good that simulation was to simulate the oil spill. With a killer poem.
miscellaneous Mon, Oct 16, 2017
Gender Gap at an International Conference on Bioinformatics
And a realization of my own unintentional conformism that is part of a bigger problem
miscellaneous Thu, Sep 14, 2017
Candidate Phyla Radiation in Human Blood?
Astonishing if its true. Astonishing if its false. Astonishments all over.
miscellaneous Wed, Aug 23, 2017
Recovering ribosomal RNA gene sequences with anvi'o
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
Microbial Dark Matter: The mullet of microbial ecology
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
A thousand microbial genomes from the TARA Oceans metagenomes
On a journey characterizing a thousand population genomes from the surface of oceans and seas
miscellaneous Sun, May 21, 2017
Importing Prokka annotations into anvi'o
If Prokka doesn't come to you, you go to Prokka
anvio Thu, May 18, 2017
An anvi'o workshop at the Joint Genome Institute
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
The new anvi'o 'news' tab
Is the big brother watching you? If he does, what does he see?
anvio Tue, May 16, 2017
Notes on genome refinement with anvi'o
More than just completion and redundancy estimates
anvio Thu, May 11, 2017
An anvi'o workshop at the University of Chicago
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
The new anvi'o BAM profiler
Has decades of suffering of thousands of anvi'o users come to an end?
anvio Tue, Mar 07, 2017
An 800-years-old Salmonella genome, and a lovely anvi'o figure
From the paper 'Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica'
miscellaneous Sun, Feb 05, 2017
Inspecting the genomic link between Archaea and Eukaryota
Curating the composite metagenome-assembled genome Lokiarchaeum sp. GC14_75 with anvi'o
miscellaneous Tue, Jan 03, 2017
Bacteroides Genome Variants, and a reproducible science exercise with anvi'o
The way we made sure everyone has access to the genomes we recovered
miscellaneous Mon, Nov 21, 2016
An anvi'o workflow for microbial pangenomics
The user-friendly interface anvi'o provides to work with pangenomes.
anvio Tue, Nov 08, 2016
Working with SVG files anvi'o generate
In other words, not putting screenshots in papers
anvio Thu, Oct 27, 2016
Annotating an anvi'o contigs database with COGs
Yes. Good ol' COGs. Into your contigs db. Just like that. 60% of the time, every time.
anvio Tue, Oct 25, 2016
Microbial 'omics and anvi'o workshops
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
Assessing completion and contamination of metagenome-assembled genomes
A tale from 4,000+ gold standard bacterial genomes to justify 'max 10% redundancy'
miscellaneous Thu, Jun 09, 2016
Chicago Fellows Program
A prestigious post-doc opportunity at a great university environment
miscellaneous Wed, Jun 08, 2016
Binning without mapping
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
Making anvi'o use your own HMM collection
Mike Lee demonstrates how to use a custom HMM single-copy gene profile for archaeal genomes
anvio Sat, May 21, 2016
Predicting CPR genomes in metagenomic bins
A second look at the genomes published by Brown CT. et al
miscellaneous Sun, Apr 17, 2016
SF, SD, LA. Going places, meeting people.
Musings from my recent visits to Berkeley, Stanford, USC, and SDSU
miscellaneous Fri, Apr 08, 2016
The anvi'o interactive interface
Data types, usage tips, and other stuff about the interface
anvio Sat, Feb 27, 2016
A short journey into a metagenomic dataset
Musings over a *Nitrospira* genome that can do complete nitrification
anvio Wed, Dec 09, 2015
How many bacterial genomes do you have in that assembly?
A quick way to get an insight into the number of genomes your contigs represent.
anvio Mon, Dec 07, 2015
Running the interactive interface through an SSH tunnel
For people who does not have time to download stuff.
anvio Sat, Nov 28, 2015
An anvi'o workflow for microbial pangenomics (old version)
The user-friendly interface anvi'o provides to work with pangenomes.
anvio Sat, Nov 14, 2015
OS X installer for anvi'o
Do you want to try anvi'o? Do you have a MAC computer? We got you covered.
anvio Thu, Aug 20, 2015
Studying microbial population genetics with anvi'o
Exploring micro-diversity patterns using for deeper insights into ecology
anvio Mon, Jul 20, 2015
Removing contaminants from cultivars with anvi'o
Anvi'o provides an interface to screen for possible contaminants and curate individual genomes
anvio Thu, Jun 25, 2015
Comparing different mapping software using anvi'o
Bowtie, Bowtie2, BWA, CLC, GSNAP, BBMap, Novoalign, and SMALT.
anvio Tue, Jun 23, 2015
Combining metagenomics with metatranscriptomics
Tricks for people who like to go deeper.
anvio Wed, Jun 10, 2015
Post-doc opportunity in France at LM2E
Life at the extremes: microbial EcoGenomics of deep-sea extremophiles
miscellaneous Fri, May 22, 2015
Refining a bin using anvi'o
Dealing with heavily contaminated bins identified in an unsupervised manner.
anvio Mon, May 11, 2015
High-Resolution Microbiome Informatics Meeting, 2015
A small-scale meeting to make a statement about high-resolution.
oligotyping Sat, Mar 14, 2015
New insights into microbial ecology through subtle nucleotide variation
A summary of the oligotyping special topic in Frontiers In Microbiology
oligotyping Thu, Feb 12, 2015
Minimum Entropy Decomposition: A new clustering algorithm
1nt resolution at marker gene analyses!
Tue, Nov 04, 2014
Oligotyping and alignment
Answers to some of the questions that have been asked frequently
oligotyping Sun, Sep 14, 2014
A Docker image for oligotyping
For people who does not want to install the pipeline
oligotyping Tue, Sep 02, 2014
Installing the oligotyping pipeline
Installing the pipeline shall not be a PITA.
oligotyping Sat, Aug 16, 2014
Oligotyping analysis of the human oral microbiome
In which we oligotyped the entire oral microbiome data generated by the HMP...
oligotyping Wed, Jun 25, 2014
Frontiers in Microbiology Special Topic
A special topic for oligotyping
oligotyping Thu, Dec 12, 2013
Methods paper for oligotyping is out!
It is published in Methods in Ecology and Evolution...
oligotyping Wed, Oct 16, 2013
Network analysis of the human oral microbiota using oligotypes
The oligotyping pipline generates Gephi-compatible network descriptions.
oligotyping Fri, Mar 29, 2013
Sewage reflects the distribution of human faecal Lachnospiraceae
A study that shows the connection between human microbiome and the sewage
oligotyping Thu, Feb 28, 2013
Basic sample mapping with oligotyping
If you have a categorical mapping file, the oligotyping pipeline can deliver more
oligotyping Mon, Feb 04, 2013
Oligotyping Pipeline Explained
How to install, and how to start using the oligotyping pipeline
oligotyping Fri, May 11, 2012
A Success Story: Gardnerella Vaginalis Profiles Among Sexual Partners
The first story we recovered using oligotyping
oligotyping Wed, May 02, 2012