ctb
Prof at UC Davis. Blogs at http://ivory.idyll.org/blog/ and uses bluesky under ctitusbrown.
University of California, DavisDavis, CA
Pinned Repositories
2013-pycon-awesome-big-data-algorithms
2019-snakemake-ucdavis
Intro to workflows for efficient automated data analysis, using snakemake.
advanced-swc
Intermediate and Advanced Software Carpentry tutorial material
figleaf
A code coverage recording and analysis tool for Python
pony-build
A simple continuous integration system, written in Python.
twill-legacy
A simple command-line Web browser, for testing and Web automation.
charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
genome-grist
map Illumina metagenomes to genomes!
sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
spacegraphcats
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
ctb's Repositories
ctb/titus-blog
My blog.
ctb/2024-human-contam
Explore microbial contamination in human whole-genome shotgun data sets, using sourmash
ctb/2024-sourmash-example-plots
Some example plots for sourmash
ctb/2024-sourmash-richness-and-diversity
ctb/pp-sketchlib
Library of sketching functions used by PopPUNK
ctb/2023-equitable-efficient
ctb/2023-jean-zhao-read-coverage
ctb/2024-assembly-tax-loss
ctb/2024-debug-gather-difference
ctb/2024-ebi-mgnify-rest
ctb/2024-ggg-298-lab7
ctb/2024-ggg-298-lab7-test
ctb/2024-ggg-298-quarto
ctb/2024-ggg-298-quarto-test
ctb/2024-human-sketch
Use sourmash to sketch the human genome (hg38), incl all unmapped chromosomes.
ctb/2024-mkdocs-datalab-tea
demo of mkdocs
ctb/2024-pangenome-hash-corr
ctb/2024-snakemake-delete
Odd behavior of `snakemake --delete-all-output`
ctb/2024-sourmash-cds-coverage
ctb/2024-summarize-assembly-mapping
ctb/assembly-exercise
Shotgun sequencing of text, in CGI script form
ctb/cuttlefish
Building the compacted de Bruijn graph efficiently from references or reads.
ctb/d-rug.github.io
Davis R Users' Group website
ctb/farm-docs
ctb/minia
Minia is a short-read assembler based on a de Bruijn graph
ctb/oxli-feedstock
A conda-smithy repository for oxli.
ctb/pyodide
Pyodide is a Python distribution for the browser and Node.js based on WebAssembly
ctb/sourmash_plugin_branchwater-feedstock
A conda-smithy repository for sourmash_plugin_branchwater.
ctb/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
ctb/stamps_2024_assembly_tutorial
Tutorials for STAMPS 2024 related to metagenome QC, assembly and multiple genome alignment