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.
Snaps are applications packaged with all their dependencies to run on all popular Linux distributions from a single build. They update automatically and roll back gracefully.
Snaps are discoverable and installable from the Snap Store, an app store with an audience of millions.
Snap is available for Linux Mint 18.2 (Sonya), Linux Mint 18.3 (Sylvia), Linux Mint 19 (Tara), Linux Mint 19.1 (Tessa) and the latest release, Linux Mint 20 (Ulyana).
You can find out which version of Linux Mint you’re running by opening System info from the Preferences menu.
On Linux Mint 20, /etc/apt/preferences.d/nosnap.pref needs to be removed before Snap can be installed. This can be accomplished from the command line: