Table 1.

Options available in Hound, as shown by the command HoundAnalyser–help

Flag	Description
-h, —help	Show this help message and exit
—preprocess FILE DIRNAME
	Unzip Illumina reads and create appropriate directory structure. It requires a name to create destination directory. REQUIRED unless —project is given.
—project DIR	Directory where FASTQ files can be found. It can be a directory of directories if FASTQ files are contained in a ‘reads’ directory. Maximum directory depth is 2. REQUIRED unless —preprocess is given.
—assemble	Assemble reads. Requires —project.
—reference FILE	Reference genome in FASTA format. Requires —assemble.
—de-novo	Assemble reads de novo. Used to assemble genomes and specify assembly type for data analysis. Requires —assemble.
—coverage	Compute coverage depth to estimate gene copy number. Can be used to assemble genomes or include coverage depth in the data analysis. Requires —hk-genes.
—hk-genes FILE	List of Multilocus sequence typing (MLST) genes, or other reference genes, in FASTA format to compute baseline coverage depth. Requires —coverage.
—genes FILE	List of genes to be found, in FASTA format. Requires —identity and —prefix.
—genes-dir DIR	Directory containing genes of interest in FASTA format. Requires —summary.
—nucl	Use nucleotide sequences for the search. Requires —genes.
—prefix NAME	Label added to all output files. Required to do multiple searches with the same assemblies.
—identity NUM NUM	Identity threshold required to shortlist sequences found. Two floats (min identity, max identity) between 0 and 1 are required. Requires—genes.
—promoter	Isolate the promoter region of the target gene(s) sequences found and ignore coding sequences. Requires —cutoff.
—cutoff NUM	Length of the promoter in nucleotides. Requires —promoter.
—phylo	Align sequences of promoter/coding sequences found, and generate the corresponding phylogeny.
—phylo-thres NUM	Remove sequences that are a fraction of the total size of alignment. Used to improve quality alignment. Requires a number between 0 and 1 (defaults to 0.5).
—plot FILE	Generate plot from the multiple alignment of sequences found, and save as FILE.
—roi FILE	Sequences of interest to look for in the gene(s) found, in FASTA format. Requires—plot.
—summary FILE	Save Hound analysis as a spreadsheet. Requires—project.
—labels FILE	XLS file containing assembly name (col 1), and assembly type (col 6) to label phylogeny leafs (defaults to assembly name). Requires —plot.
—force	Force re-generation of phylogeny and/or plot even if they already exist.