Evolution of a cover (Sun, Sep 22, 2024, by meren)

From a vague idea to a piece of art miscellaneous

Research week at BIOS: Getting my hands wet with data (Sat, Apr 08, 2023, by matt)

Matt's first time sampling water from a CTD miscellaneous

Binning giant viruses and their close relatives with anvi'o (Mon, Jan 03, 2022, by tom)

A journey into the genomics of giant viruses and their close relatives miscellaneous

Targeted binning of a novel nitrogen-fixing population from the Arctic Ocean (Wed, Oct 20, 2021, by iva)

Using metabolism estimation to go fishing in some ocean metagenomes. miscellaneous

From Boats to Bits: Evolution of a study on marine microbes (Mon, Sep 13, 2021, by meren)

Or, Meren's personal notes from a 48 hours, high-resolution, diel sampling effort in Hawai'i. miscellaneous

Mentorship in life sciences: voices of mentees (Tue, Jun 01, 2021, by meren)

An attempt to learn from the experiences of ECRs with their mentors miscellaneous

Poor Man's Redirect (Fri, May 28, 2021)

A reading list for scientists to recognize and confront anti-Black racism (Mon, Oct 05, 2020, by andrea)

miscellaneous

The history of metagenomics: An incomplete summary (Mon, Jul 27, 2020, by matt)

A personal and directed look at the past of an exciting discipline. miscellaneous

Estimating per-residue binding frequencies with InteracDome (Wed, Jul 22, 2020, by evan)

A blog post detailing InteracDome's integration into anvi'o anvio

Welcome to the dark side of genomes and metagenomes (Wed, Jul 01, 2020, by antonio)

On how we unified the known and unknown CDS-space in genomes and metagenomes miscellaneous

Online seminar series on Microbial 'Omics for beginners (Sat, Jun 27, 2020, by meren)

Socially isolated community discussions on key concepts and stuff. miscellaneous

Visualizing the fate of contigs across metagenomic binning algorithms (Thu, Jan 02, 2020, by meren)

Don't click. Run away. Don't see what you don't want to see. miscellaneous

To dereplicate or not to dereplicate? (Thu, Dec 12, 2019, by jacob_e)

Inflating the number of near-identical genomes versus losing potentially key genetic information in genome-resolved metagenomics studies. miscellaneous

Visualizing contig coverages to better understand microbial population structures (Mon, Nov 25, 2019, by emily)

Ways to visualize mapping results in anvi'o to make informed statements about environmental populations and to generate high-quality figures) anvio

Extract loci from genomes and metagenomes with anvi'o (Thu, Oct 17, 2019, by matt)

A flexible and scalable approach to locate and extract target genetic loci from larger genetic contexts. anvio

Genome / metagenome / MAG taxonomy with anvi'o (Tue, Oct 08, 2019, by meren)

An attempt at alchemy combining the magic of GTDB and single-copy core genes in anvi'o. anvio

Getting help from the anvi'o community (Mon, Oct 07, 2019, by iva)

A primer on how to find your way through the maze of microbial 'omics and anvi'o anvio

Accessing and including NCBI genomes in 'omics analyses in anvi'o (Thu, Mar 14, 2019, by alon)

How to download, process, and combine genomes from NCBI in your phylogenomic, pangenomic, and/or other 'omics analyses anvio

An interdisciplinary Wolbachia story through connections across the Atlantic: Metagenomics, long-read sequencing, and other things (Tue, Mar 05, 2019, by julie)

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... miscellaneous

Fantastic Data and How to Share Them: A Plea to Journal Editors and Reviewers (Sun, Feb 24, 2019, by meren)

A small checklist for reviewers to follow to make public data sources public and forever miscellaneous

My unpopular two cents on the 'Face on a Turd' (Mon, Dec 17, 2018, by meren)

One of those 'I can not believe you are even considering reading this' posts miscellaneous

Combining reference genome annotations with your own in pangenomes (Sat, Dec 01, 2018, by mike)

Mike Lee heroically combines reference annotations with new annotations anvio

Microbial 'Omics Workshop (Sun, Sep 09, 2018, by alon)

A light introduction to questions of microbial ecology and microbial omics through the story of crassphage anvio

Integrating sequence variants and predicted protein structures (Tue, Sep 04, 2018, by evan)

A discussion on the practical and theoretical aspects of using anvi'o structure anvio

Anvi'o snakemake workflows (Mon, Jul 09, 2018, by alon)

Bringing the magic of anvi'o together with the wonders of snakemake. anvio

Assessing the completion of eukaryotic bins with anvi'o (Sat, May 05, 2018, by tom)

A preliminary set of 83 HMMs from BUSCO. -Lol is anvi'o doing picoeuks now fam? -Why yes, yes it does. anvio

Running remote anvi'o interactive interfaces on your local computer (Wed, Mar 07, 2018, by ozcan)

A hacker's guide to anvi'o networking. Are you scared? You should be! anvio

Amino acid color coding by conservation in anvi'o gene clusters (Tue, Feb 13, 2018, by mahmoud)

Details of a beautiful algorithm. anvio

Importing VirSorter annotations into anvi'o to study phages (Thu, Feb 08, 2018, by bryan)

Anvi'o projects meet the underappreciated owners of this planet. anvio

Getting ribosomal RNA gene sequences from a MinION run (Thu, Jan 18, 2018, by meren)

We just started playing with this, we have no idea what we are doing. Kthxbye. miscellaneous

Importing GhostKOALA/KEGG annotations into anvi'o (Wed, Jan 17, 2018, by elaina)

KEGG modules, meet anvi'o. Anvi'o, meet KEGG modules. anvio

An anvi'o workshop at the University of California, Irvine (Mon, Dec 25, 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

Working with anvi'o additional data tables (Mon, Dec 11, 2017, by meren)

Getting additional data in an out of pan and profile databases like a pro. anvio

DWH O. desum v2: Most abundant Oceanospirillaceae population in the Deepwater Horizon Oil Plume (Sat, Nov 25, 2017, by tom)

Dotting i's and crossing t's with this Deepwater Horizon oil plume drama. miscellaneous

Ca. Bermanella macondoprimitus is not a strain variant of the oil plume (Reply to Probst et al.) (Mon, Oct 16, 2017, by meren)

Continuing to investigate how good that simulation was to simulate the oil spill. With a killer poem. miscellaneous

Gender Gap at an International Conference on Bioinformatics (Thu, Sep 14, 2017, by meren)

And a realization of my own unintentional conformism that is part of a bigger problem miscellaneous

Candidate Phyla Radiation in Human Blood? (Wed, Aug 23, 2017, by meren)

Astonishing if its true. Astonishing if its false. Astonishments all over. miscellaneous

Recovering ribosomal RNA gene sequences with anvi'o (Sun, Jul 09, 2017, by meren)

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

Microbial Dark Matter: The mullet of microbial ecology (Thu, Jun 22, 2017, by meren)

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

An anvi'o workflow for phylogenomics (Wed, Jun 07, 2017, by meren)

That is easy, but not simple anvio

A thousand microbial genomes from the TARA Oceans metagenomes (Sun, May 21, 2017, by tom)

On a journey characterizing a thousand population genomes from the surface of oceans and seas miscellaneous

Importing Prokka annotations into anvi'o (Thu, May 18, 2017, by antti)

If Prokka doesn't come to you, you go to Prokka anvio

An anvi'o workshop at the Joint Genome Institute (Wed, May 17, 2017, by meren)

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

The new anvi'o 'news' tab (Tue, May 16, 2017, by meren)

Is the big brother watching you? If he does, what does he see? anvio

Notes on genome refinement with anvi'o (Thu, May 11, 2017, by veronika)

More than just completion and redundancy estimates anvio

Anvi'o 'views' demystified (Mon, May 08, 2017, by mike)

Mike Lee heroically demystifies the view options anvio

An anvi'o workshop at the University of Chicago (Thu, Mar 23, 2017, by meren)

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

The new anvi'o BAM profiler (Tue, Mar 07, 2017, by meren)

Has decades of suffering of thousands of anvi'o users come to an end? anvio

An 800-years-old Salmonella genome, and a lovely anvi'o figure (Sun, Feb 05, 2017, by meren)

From the paper 'Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica' miscellaneous

Inspecting the genomic link between Archaea and Eukaryota (Tue, Jan 03, 2017, by tom)

Curating the composite metagenome-assembled genome Lokiarchaeum sp. GC14_75 with anvi'o miscellaneous

Wavy coverage patterns in mapping results (Wed, Dec 14, 2016, by meren)

Coverage, why you do dis? miscellaneous

Bacteroides Genome Variants, and a reproducible science exercise with anvi'o (Mon, Nov 21, 2016, by meren)

The way we made sure everyone has access to the genomes we recovered miscellaneous

An anvi'o workflow for microbial pangenomics (Tue, Nov 08, 2016, by meren)

The user-friendly interface anvi'o provides to work with pangenomes. anvio

Working with SVG files anvi'o generate (Thu, Oct 27, 2016, by meren)

In other words, not putting screenshots in papers anvio

Annotating an anvi'o contigs database with COGs (Tue, Oct 25, 2016, by meren)

Yes. Good ol' COGs. Into your contigs db. Just like that. 60% of the time, every time. anvio

Microbial 'omics and anvi'o workshops (Thu, Aug 18, 2016, by meren)

A resource to find out whether we are coming to or you just missed an event close to a location near you. anvio

I dub thee MBL Fellow (Tue, Jul 12, 2016, by meren)

Marine Biological Laboratory and I. miscellaneous

Installation V2 (Sun, Jun 26, 2016)

Anvi'o User Tutorial for Metagenomic Workflow (Wed, Jun 22, 2016)

Sweets for people who managed to install the platform and want to do genome-resolved metagenomics. anvio

Installing third-party software (Sat, Jun 18, 2016)

Recipes to install various software tools anvi'o uses anvio

Importing taxonomy into contigs database (Sat, Jun 18, 2016)

Various ways to add the taxonomic annotations into anvi'o anvio

Importing functions into contigs database (Sat, Jun 18, 2016)

Making those functions in the summary output bloom with stuff! anvio

Assessing completion and contamination of metagenome-assembled genomes (Thu, Jun 09, 2016, by meren)

A tale from 4,000+ gold standard bacterial genomes to justify 'max 10% redundancy' miscellaneous

Chicago Fellows Program (Wed, Jun 08, 2016, by meren)

A prestigious post-doc opportunity at a great university environment miscellaneous

Binning without mapping (Mon, Jun 06, 2016, by meren)

So you have an assembly, or a draft genome, or a MAG, but no metagenomic short reads? That's OK. anvio

Making anvi'o use your own HMM collection (Sat, May 21, 2016, by mike)

Mike Lee demonstrates how to use a custom HMM single-copy gene profile for archaeal genomes anvio

Predicting CPR genomes in metagenomic bins (Sun, Apr 17, 2016, by meren)

A second look at the genomes published by Brown CT. et al miscellaneous

SF, SD, LA. Going places, meeting people. (Fri, Apr 08, 2016, by meren)

Musings from my recent visits to Berkeley, Stanford, USC, and SDSU miscellaneous

An anvi'o workshop in Montréal (August 29 and 30, 2016) (Sun, Mar 13, 2016)

In case you would like to stick around a bit longer after ISME miscellaneous

The anvi'o interactive interface (Sat, Feb 27, 2016, by meren)

Data types, usage tips, and other stuff about the interface anvio

Post-doc positions available (Thu, Dec 17, 2015)

At the Department of Medicine, University of Chicago miscellaneous

A short journey into a metagenomic dataset (Wed, Dec 09, 2015, by meren)

Musings over a *Nitrospira* genome that can do complete nitrification anvio

How many bacterial genomes do you have in that assembly? (Mon, Dec 07, 2015, by meren)

A quick way to get an insight into the number of genomes your contigs represent. anvio

Running the interactive interface through an SSH tunnel (Sat, Nov 28, 2015, by meren)

For people who does not have time to download stuff. anvio

An anvi'o workflow for microbial pangenomics (old version) (Sat, Nov 14, 2015, by meren)

The user-friendly interface anvi'o provides to work with pangenomes. anvio

Docker image for anvi'o (Sat, Aug 22, 2015, by meren)

Fresh anvi'o builds for the lazy. anvio

OS X installer for anvi'o (Thu, Aug 20, 2015, by meren)

Do you want to try anvi'o? Do you have a MAC computer? We got you covered. anvio

Studying microbial population genetics with anvi'o (Mon, Jul 20, 2015, by meren)

Exploring micro-diversity patterns using for deeper insights into ecology anvio

Removing contaminants from cultivars with anvi'o (Thu, Jun 25, 2015, by tom)

Anvi'o provides an interface to screen for possible contaminants and curate individual genomes anvio

Comparing different mapping software using anvi'o (Tue, Jun 23, 2015, by meren)

Bowtie, Bowtie2, BWA, CLC, GSNAP, BBMap, Novoalign, and SMALT. anvio

Combining metagenomics with metatranscriptomics (Wed, Jun 10, 2015, by meren)

Tricks for people who like to go deeper. anvio

Post-doc opportunity in France at LM2E (Fri, May 22, 2015, by meren)

Life at the extremes: microbial EcoGenomics of deep-sea extremophiles miscellaneous

Refining a bin using anvi'o (Mon, May 11, 2015, by meren)

Dealing with heavily contaminated bins identified in an unsupervised manner. anvio

Anvi'o User Tutorial for Metagenomic Workflow (v1) (Sat, May 02, 2015)

Sweets for people who managed to install the platform. anvio

Installing anvi'o (v1) (Fri, May 01, 2015)

Instructions to install the v1 brach of the platform. anvio

High-Resolution Microbiome Informatics Meeting, 2015 (Sat, Mar 14, 2015, by meren)

A small-scale meeting to make a statement about high-resolution. oligotyping

New insights into microbial ecology through subtle nucleotide variation (Thu, Feb 12, 2015, by meren)

A summary of the oligotyping special topic in Frontiers In Microbiology oligotyping

Minimum Entropy Decomposition: A new clustering algorithm (Tue, Nov 04, 2014, by meren)

1nt resolution at marker gene analyses!

From QIIME to Oligotyping (Thu, Oct 16, 2014, by meren)

A solution by James Meadow oligotyping

Oligotyping and alignment (Sun, Sep 14, 2014, by meren)

Answers to some of the questions that have been asked frequently oligotyping

A Docker image for oligotyping (Tue, Sep 02, 2014, by meren)

For people who does not want to install the pipeline oligotyping

Installing the oligotyping pipeline (Sat, Aug 16, 2014, by meren)

Installing the pipeline shall not be a PITA. oligotyping

Oligotyping analysis of the human oral microbiome (Wed, Jun 25, 2014, by meren)

In which we oligotyped the entire oral microbiome data generated by the HMP... oligotyping

Frontiers in Microbiology Special Topic (Thu, Dec 12, 2013, by meren)

A special topic for oligotyping oligotyping

How to oligotype: Best practices (Mon, Nov 04, 2013, by meren)

Flowchart of oligotyping... oligotyping

Methods paper for oligotyping is out! (Wed, Oct 16, 2013, by meren)

It is published in Methods in Ecology and Evolution... oligotyping

Network analysis of the human oral microbiota using oligotypes (Fri, Mar 29, 2013, by meren)

The oligotyping pipline generates Gephi-compatible network descriptions. oligotyping

Sewage reflects the distribution of human faecal Lachnospiraceae (Thu, Feb 28, 2013, by meren)

A study that shows the connection between human microbiome and the sewage oligotyping

Basic sample mapping with oligotyping (Mon, Feb 04, 2013, by meren)

If you have a categorical mapping file, the oligotyping pipeline can deliver more oligotyping

Oligotyping Pipeline Explained (Fri, May 11, 2012, by meren)

How to install, and how to start using the oligotyping pipeline oligotyping

A Success Story: Gardnerella Vaginalis Profiles Among Sexual Partners (Wed, May 02, 2012, by meren)

The first story we recovered using oligotyping oligotyping