---
title: Install pathogenie on Pop!_OS using the Snap Store | Snapcraft
description: Get the latest version of pathogenie for on Pop!_OS - microbial genome
  annotation and gene finding tool
url: https://snapcraft.io/install/pathogenie/pop
---

[Canonical Snapcraft](https://snapcraft.io/)

# Install pathogenie on **Pop!\_OS**

# pathogenie

[Damien Farrell (dmnfarrell)](https://snapcraft.io/publisher/dmnfarrell "View all snaps from Damien Farrell (dmnfarrell)")

* [Damien Farrell (dmnfarrell)](https://snapcraft.io/publisher/dmnfarrell "View all snaps from Damien Farrell (dmnfarrell)")
* [Science](https://snapcraft.io/search?categories=science)

[Install](https://snapcraft.io/install/pathogenie/pop#install)

#### microbial genome annotation and gene finding tool

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.

### Package name

* pathogenie

---

### License

* GPL-3.0+

---

### Last updated

* 31 January 2021 - latest/beta

This snap hasn't been updated in a while. It might be unmaintained and have stability or security issues.

---

### Websites

* [github.com/dmnfarrell/pathogenie](https://github.com/dmnfarrell/pathogenie "https://github.com/dmnfarrell/pathogenie")

---

### Contact

* [github.com/dmnfarrell](https://github.com/dmnfarrell "https://github.com/dmnfarrell")

---

##### Report a Snap Store violation

* [Report this Snap](https://snapcraft.io/install/pathogenie/pop#report-snap-modal)

---

## Enable snaps on Pop!\_OS and install pathogenie

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](https://snapcraft.io/store), an app store with an audience of millions.

### Enable snapd

Snap can be installed on Pop!\_OS from the command line. Open Terminal from the Applications launcher and type the following:

```
sudo apt update
sudo apt install snapd
```

Either log out and back in again, or restart your system, to ensure snap’s paths are updated correctly.

### Install pathogenie

To install pathogenie, simply use the following command:

```
sudo snap install pathogenie --beta
```

### Other popular snaps…

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[See more in Featured](https://snapcraft.io/search?categories=featured)

### More things to do…

#### [Get the snap store](https://snapcraft.io/snap-store)

Browse and find snaps from the convenience of your desktop using the snap store snap.

#### [Learn more about snaps](https://snapcraft.io/docs)

Interested to find out more about snaps? Want to publish your own application? Visit [snapcraft.io](https://snapcraft.io/) now.

[Back to top](https://snapcraft.io/install/pathogenie/pop)

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