Project

bacterial-annotator

0.0
Low commit activity in last 3 years
A long-lived project that still receives updates
bacterial-annotatorzorino/bacterial-annotatorHomepageDocumentationSource CodeBug TrackerWiki
GEM to annotate bacterial genome sequence based on a reference genome and complete the annotation with an external database.
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
 Popularity
Downloads
104,759
Stars
2
Forks
1
Watchers
3
 Releases
Current version
1.0.0
Total releases
53
First release
2015-02-24
Latest release
2024-01-13
 Issues
Open Issues
1
Closed Issues
1
Total Issues
2
Issue Closure Rate
50%
 Pull Requests
Open Pull Requests
0
Closed Pull Requests
0
Merged Pull Requests
1
Pull Request Acceptance Rate
100%
 Development
Primary Language
Ruby
Licenses
GPL-3.0
Average date of last 50 commits
2019-02-28
Reverse Dependencies
0

 Dependencies

Runtime

bio
~> 1.4, >= 1.4.3
mechanize
~> 2.7, >= 2.7.3
parallel
~> 1.9, >= 1.9.0
 Project Readme

Bacterial-Annotator GEM

Ruby GEM to annotate bacterial genomes based on a reference genome and also complete the annotation with external or remote databases.

To install the gem locally with this package

gem build bacterial-annotator.gemspec
gem install bacterial-annotator-0.0.1.gem

bacterial-annotator -h

Or you could simply install it from rubygems.org with that command

gem install bacterial-annotator

The blat aligner and the prodigal ORF finder will be installed as dependencies if you accept their licenses.

Example of usage

  • Bacterial genome annotation
bacterial-annotator annotate -i my_genome.fasta -g reference_genome.gbk -o annotation_output_dir --pidentity 80 --pcoverage 90

# reference_genome.gbk could also only be the genome ID which will be fetched from NCBI
  • Bacterial genome comparison
# in a folder where you want to compare diffente genome annotations
bacterial-annotator compare --refgenome reference_genome.gbk --pidentity 80 --align prot --phylogeny --software fasttree *.gbk