sourmash tax for taxonomic classification and metagenome breakdown
Note: The tax module was developed with Titus Brown, Taylor Reiter, Luiz Irber, and Hannah Houts. The approaches described have emerged over years of sour...
All Posts
2021
2020
No Lab, No Problem? Our experience as part of NSURP, 2020
Like many folks, our ability to host in-person training and research projects evaporated for summer 2020. Unlike many folks, our bioinformatics research is e...
Tips and Tricks for running snakemake on our HPC (farm)
These are notes for a virtual in-lab learning opportunity (vILLO) in the lab for data-intensive biology at UC Davis (08/24/2020). The main goal is to pass al...
Biased Policing in San Diego
We shouldn’t need statistics (or videos) to believe our fellow humans about their lived experiences. But sometimes data can highlight the glaring differences...
Deploying Mkdocs via Github Actions
I need to edit some documentation for our workflow projects dammit and elvers. These docs are set up in mkdocs, which I love for it’s simplicity: I can write...
Using snakemake `--profile` for default settings and cluster execution
There are a number of parameters I always want to run for snakemake, and writing them on the command line every time can be tedious. For example, I nearly al...
2019
snakemake & slurm
Snakemake can submit each of your jobs to the slurm scheduler for you! To enable this, you need to provide the --cluster option to snakemake on the command l...
Editing Documentation Compiled via Mkdocs
Most of my documentation is written in markdown (.md files) and built into an html site by mkdocs. If you want to edit any of these documents, you can make c...
Setting up MkDocs in a new repo
In your repo:
Metatranscriptomics workshop & development
by N. Tessa Pierce and Taylor Reiter
2018
On Snakemake and wrappers for workflows
A few months ago, Titus wrote about the dib-lab’s slow creep into the world of snakemake for workflow applications. Thanks to some good examples and a lot of...
2017
Starting Postdoc
I'm starting a postdoc in the Data Intensive Biology Lab at UC Davis, run by Titus Brown. I’m kicking it off as an instructor at DIBSI!
2015
Software Carpentry
Teaching my first software carpentry workshop at UCSD next week! More info here.