Quick start guide

Installation

Follow the guidelines in the section Installation

Running the analysis

1. Create a configuration file using the following template and adapt it to fit your data.

fasta_path: "path/to/assembly.fasta" # path to assembly FASTA
gff_path: "path/to/assembly.gff" # path to annotation in GFF3 format
output_path: "path/to/output_directory/" # directory to save results in
taxon_id: "<NCBI taxon ID>" # NCBI Taxon ID of query species

2. To include coverage information, add the path to a sorted bam file (this is optional). Otherwise, omit this parameter from the configuration file.

bam_path_1: "path/to/mapping.bam"

• Note: When using multiple coverage sets, duplicate the parameter and increase the number in the suffix

3. To provide pre-compiled protein sequences, specify the path to the FASTA. For details on format requirements see the section Input data

proteins_path: "path/to/proteins.faa"

To run taXaminer, call it with the path to the config file, like so:

taxaminer.run <config.yml>

For details on additional options see Configuration parameters.