Identify the Brucella species of a fastq sample by its MASH distance to 429 curated reference genomes, covering all 30 named species of the clade, and type it with the nine-locus Whatmore MLST scheme.
This page exists for one reason: GitHub serves an HTML file in a repository as source code rather than rendering it, and the quality assurance report is easier to judge by looking at it.
Example quality assurance report → A real run of the four public read sets of the tutorial, including the B. canis sample whose species the sequence type decides, with the machine it ran on removed. One self-contained file: no script, no stylesheet, no font, nothing fetched from anywhere. It prints one sample to a page. The same report as a PDF → What--pdf writes: the same evidence laid out for paper, one sample to a page, with
the page number in every footer so a loose sheet can be placed.
Everything else
- The repository
- The wiki: installation, a tutorial on public read sets, usage, output files, how it works, validation and the FAQ
- brucellaid on PyPI —
pip install brucellaid - Zenodo, for the DOI of each release