pathogenie

pathogenie

Damien Farrell (dmnfarrell) Publisher
  • Damien Farrell (dmnfarrell) Publisher
  • Science

Install latest/beta of pathogenie

Ubuntu 16.04 or later?

Make sure snap support is enabled in your Desktop store.


Install using the command line

sudo snap install pathogenie --beta

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pathogenie is only available on the unstable beta channel. It could break and change often.

Channel Version Published

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.

Developer website

Contact Damien Farrell

Details for pathogenie

License
GPL-3.0+
Last updated
31 January 2021

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Where people are using pathogenie

Users by distribution (log)

Ubuntu 20.04
Ubuntu 21.04

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