The PhD repo

Qualifying Exam

Exam happened in 2019-04-17.

• Proposal
• Presentation

Dissertation

Uses aggiedown and GitHub Actions for CI. Tagged versions are available in the Releases page.

Experiments

smol gather

experiments/smol_gather

Comparison of containment approaches using MinHash:

• CMash (containment minhash)
• mash screen
• smol (scaled minhash)

Regenerating results (after running the setup steps):

conda activate thesis
cd experiments/smol_gather && snakemake --use-conda

Scaled MinHash sizes

experiments/sizes

Scaled MinHash sizes (number of hashes) analysis across domains in Genbank.

Inverted index and shared hashes

experiments/lca

Analyzing unique and shared hashes in an inverted index.

Setup

All processing and analysis scripts were performed using the conda environment specified in environment.yml. To build and activate this environment run:

conda env create --force --file environment.yml

conda activate thesis