pathogenie is a desktop and command line program for annotating draft bacterial
and viral genomes. It may also be used for quickly detecting arbitrary sequences such
as antibiotic resistance genes (AMR) proteins in nucleotide sequences. It uses Blast
to find hits to known gene sequences from sequence databases. The inputs are fasta files.
Annotation is performed in a similar manner to Prokka and first requires an assembled
genome if you have sequenced reads.
From the GUI you may load fasta files into a table and then run genome annotation or gene finding with custom databases. This program utilizes the sequence databases for gene finding compiled by abricate.
This program is under development. Suggestions are welcome.
The packages for RHEL 8 and RHEL 7 are in each distribution’s respective Extra Packages for Enterprise Linux (EPEL) repository. The instructions for adding this repository diverge slightly between RHEL 8 and RHEL 7, which is why they’re listed separately below.
The EPEL repository can be added to RHEL 8 with the following command: