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.
Swap out openSUSE_Leap_15.2 for openSUSE_Leap_15.1, openSUSE_Leap_15.0, or openSUSE_Tumbleweed if you’re using a different version of openSUSE.
With the repository added, import its GPG key:
sudo zypper --gpg-auto-import-keys refresh
Finally, upgrade the package cache to include the new snappy repository:
sudo zypper dup --from snappy
Snap can now be installed with the following:
sudo zypper install snapd
You then need to either reboot, logout/login or source /etc/profile to have /snap/bin added to PATH.
Additionally, enable and start both the snapd and the snapd.apparmor services with the following commands: