Living in an Ivory Basement
Announcing taxburst, an update of the Krona software for taxonomy exploration
Announcing: the chill-filter Web site - DNA sample composition at a glance!
Why Rust is an increasingly beloved part of my programming toolbox
Recent advances in the sourmash ecosystem (August 2024)
Speeding sourmash the heck up
The history of the "Tragedy of the Commons"
Sourmash and branchwater licensing: thoughts on extractive engagement with projects
snakemake for doing bioinformatics - inputs and outputs and more!
snakemake for doing bioinformatics - using wildcards to generalize your rules
conda & mamba on shared clusters works better now!
A brief overview of automation and parallelization options in UNIX/on an HPC
snakemake for doing bioinformatics - a beginner's guide (part 2)
snakemake for doing bioinformatics - a beginner's guide (part 1)
sourmash has a plugin interface!
Reading "Orwell's Roses" by Rebecca Solnit
So! You want to search all the public metagenomes with a genome sequence!
Announcing ribbity - a hacky project to build Web sites from GitHub issue trackers
The second Common Fund Data Ecosystem hackathon - May 9-13, 2022!
Storing 64-bit unsigned integers in SQLite databases, for fun and profit
The First Common Fund Data Ecosystem Hackathon
On minimum metagenome covers, and calculating them for your own data.
A bioinformatics training career panel in the DIB Lab
Using snakemake to do simple wildcard operations on many, many, many files
A biotech career panel in the DIB Lab
Scaling sourmash to millions of samples
New sourmash databases are available!
Moving sourmash towards more community engagement - a funding application
Searching all public metagenomes with sourmash
sourmash 4.1.0 released!!
sourmash 4.0 is now available! Low low cost if you buy now!
sourmash v4.0.0 release candidate 1 is now available for comment!
Transition your Python project to use pyproject.toml and setup.cfg! (An example.)
A snakemake hack for checkpoints
Improved workflows-as-applications: tips and tricks for building applications on top of snakemake
sourmash databases as zip files, in sourmash v3.3.0
Software and workflow development practices (April 2020 update)
How to give a bad online talk
Some snakemake hacks for dealing with large collections of files
Two talks at JGI in May: sourmash, spacegraphcats, and disease associations in the human microbiome.
sourmash-oddify: a workflow for exploring contamination in metagenome-assembled genomes
Finding problematic bacterial/archaeal genomes using k-mers and taxonomy
How does sourmash's lca classification routine compare with GTDB classifications?
Sourmash LCA databases now available for the GTDB taxonomy
An initial report on the Common Fund Data Ecosystem
Comparing two genome binnings quickly with sourmash
How to encourage participation in teleconferences
Using GitHub for janky project reporting - some code
Some questions and thoughts on journal peer review.
Things to think about when developing shotgun metagenome classifiers
Our submission for the NHGRI Human Genome Reference Center call