ctb

Prof at UC Davis. Blogs at http://ivory.idyll.org/blog/ and uses bluesky under ctitusbrown.

University of California, DavisDavis, CA

Pinned Repositories

2019-snakemake-ucdavis
Intro to workflows for efficient automated data analysis, using snakemake.
32 2 214
advanced-swc
Intermediate and Advanced Software Carpentry tutorial material
Language:Python76 10 728
figleaf
A code coverage recording and analysis tool for Python
Language:Python32 4 43
pony-build
A simple continuous integration system, written in Python.
Language:Python86 5 2111
theproj
Test project for software carpentry
Language:Python31 3 041
twill-legacy
A simple command-line Web browser, for testing and Web automation.
Language:Python58 12 128
charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
Language:Python56 19 1631
genome-grist
map Illumina metagenomes to genomes!
Language:Jupyter Notebook38 22 1736
sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
Language:Python493 16 1.8k80
spacegraphcats
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
Language:Standard ML117 12 26215

ctb's Repositories

ctb/titus-blog
My blog.
Language:HTML16 4 110
ctb/2025-ncbi-rest-api
Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t
Language:Python12 1 71
ctb/2025-sourmash-analyzing-genomes-and-metagenomes
An introduction to evaluating stuff with sourmash
Language:Jupyter Notebook2 1 0
ctb/2025-davis-pug-web-intro-flask
Example flask application, with some bells and whistles
Language:Python1 1 0
ctb/2022-moore-ddd-annual-report-
Language:Shell1 0
ctb/2024-chill-gtdb-subsearch
Language:Python1 0
ctb/2024-debug-gather-difference
Language:Jupyter Notebook1 01
ctb/2024-ebi-mgnify-rest
Language:Jupyter Notebook1 2
ctb/2024-jean-mgnify-gather
Language:Python1 0
ctb/2024-podar-100k
Language:Jupyter Notebook1 0
ctb/2024-snakemake-delete
Odd behavior of `snakemake --delete-all-output`
Language:Shell1 0
ctb/2024-summarize-assembly-mapping
Language:Jupyter Notebook1 01
ctb/2025-atb-small-genomes
ref https://github.com/AllTheBacteria/AllTheBacteria/issues/54
Language:Jupyter Notebook1 0
ctb/2025-explore-sourmash-gather
Language:Python1 0
ctb/2025-explore_sourmash_rocksdb
Language:Standard ML1 0
ctb/2025-ggg-201b-hw2-spreadsheet
Language:Jupyter Notebook1 0
ctb/2025-lab-web-requests-responses
Language:Jupyter Notebook1 0
ctb/2025-make-rocksdb-entire
Make combined eukaryotic, bacterial, and archaeal RocksDB database
Language:Python1 0
ctb/2025-parse-squeue
Who's being naughty, and who's being nice?
Language:Python1 01
ctb/2025-sourmash-recursive-gather
Language:Python1 0
ctb/2025-sourmash-subtract-alt-sketch
subtract database matches from sketches based on picklists, enabling alternative ksize/scaled/moltype
Language:Python1 0
ctb/assembly-exercise
Shotgun sequencing of text, in CGI script form
Language:Python3 07
ctb/branchwater
Searching large collections of sequencing data with genome-scale queries
Language:Python1 0
ctb/oxli-feedstock
A conda-smithy repository for oxli.
1 0
ctb/plot_phylo
Python package to plot a phylogenetic tree on an existing matplotlib axis.
ctb/sourmash-minimal-feedstock
A conda-smithy repository for sourmash-minimal.
Language:Shell0 0
ctb/sourmash_alternate_implementations
Implement prefetch in cpp to investigate potential speedups
Language:Standard ML0 0
ctb/sourmash_plugin_branchwater-feedstock
A conda-smithy repository for sourmash_plugin_branchwater.
Language:Shell1 0
ctb/sourmash_plugin_directsketch-feedstock
A conda-smithy repository for sourmash_plugin_directsketch.
Language:Shell0 0
ctb/workshop_r_basics
Reader for the R Basics workshop series.