1. Getting started

In this section, I will describe what does the software do ; for actual commands, head over the next section.

Prerequisites

For WISP to work, you will need :

• A set of reference genomes (downloaded from the NCBI, for instance) or a accession file (assembly_summary like).
• A genomic or metagenomic sample, in .fastq or .fna file format.

Steps

1. Download your reference genomes, and put them inside something like genomes/train.
2. [Optional] Filter out genomes you don't want for your database with utilities.py tools.
3. Use WISP utilities.py to rename those accordingly to the file system the software uses.
4. Put your unknown samples inside something like genomes/unk.
5. [Optional] Treat them if you need to with the provided utilities.py script.
6. Create the database using wisp.py, if not already created.
7. Do predictions using wisp.py.
8. [Optional] Use utilities.py to do comparative analysis, feature analysis, database analysis and more.