BrucellaID 0.1

The clone-and-run version of BrucellaID: brucellaID.py and brucellaID_methods.py, run from a clone of the
repository, identifying the Brucella species of a read set with MASH against the 16 vSNP reference genomes and
typing it with the Whatmore MLST-9 scheme through MLSTsippr.

Tagged so that analyses and scripts built on this layout keep a fixed point to refer to: everything from
v1.0.0 onwards is an installed package with a
different command line.

Running it

git clone https://github.com/duceppemo/BrucellaID
cd BrucellaID
python brucellaID.py -s /path/to/fastq_folder -d /path/to/mlst_database -o /path/to/output

The MLST database -d points at is downloaded separately with get_mlst.py (from SRST2), which fetches the
Brucella scheme from PubMLST.

What it needs

• Python 3 with OLCTools (accessoryFunctions) and
  sipprverse (MLSTsippr)
• MASH and BBTools on the PATH

What it writes

stat_alignment_summary_<date>.xlsx in the output folder: one row per strain with the closest reference genome,
the species, and the MLST sequence type.

This release also contains the dependencies/ folder — the 16 reference genomes, the MASH sketch
vsnp_reference.msh, and the 193 MB of per-reference vSNP script_dependents trees — which later versions no
longer carry in the working tree.