micronota is an open-source, BSD-licensed package to annotate microbial genomes and metagenomes.
As Python 3 matures and majority python packages support Python 3, the scientific Python community is in favor of dropping Python 2 compatibility. Thus, micronota will only support Python 3. This will allow micronota to have few dependency and avoid maintenance of Python 2 legacy code.
micronota can annotate multiple features including coding genes, prophage, CRISPR, tRNA, rRNA and other ncRNAs. It has a customizable framework to integrate additional tools and databases. Generally, the annotation can be classified into 2 categories: structural annotation and functional annotation. Structural annotation is the identification of the genetic elements on the sequence and functional annotation is to assign functions to those elements.
To install the latest release of micronota:
conda install micronotaYou can install through pip:
pip install micronotaTo install or update to the latest developping version:
pip install git+git://github.com/biocore/micronota.git
micronota relies on external packages like prodigal, aragorn, etc. for annotation. You need to install those external packages (this is implicitly installed when micronota is installed via conda). To simplify the process, you can install with conda:
conda install --file https://raw.githubusercontent.com/biocore/micronota/master/ci/conda_requirements.txt
You need to download database files:
| Databases | Supported | Download URL |
|---|---|---|
| UniRef | yes | |
| Rfam | yes | |
| ResFam | ongoing |
micronota -hmicronota annotate -i <input.fna> -o <output-dir> --out-fmt genbank --kingdom bacteriaYou can set up what annotation to run with what parameters by providing a config file when running annotation:
micronota annotate -i <input.fna> -o <output-dir> --out-fmt genbank --kingdom bacteria --config <your-config>You can modify the default config file to create your own config file.
| Features | Supported | Tools |
|---|---|---|
| coding gene | yes | Prodigal |
| tRNA | yes | Aragorn |
| ncRNA | yes | Infernal + Rfam |
| CRISPR | yes | MinCED |
| rho-independent transcription terminator | yes | transtermhp |
| tandem repeat | yes | tandem repeat finder (trf) |
| ribosomal binding sites | ongoing | RBSFinder |
| prophage | ongoing | PHAST |
| replication origin | todo | Ori-Finder 1 (bacteria) & Ori-Finder 2 (archaea) |
| microsatellites | todo | nhmmer? |
| signal peptide | ongoing | SignalP |
| transmembrane proteins | ongoing | TMHMM |
If you’re interested in getting involved in micronota development, see CONTRIBUTING.md.
See the list of micronota’s contributors.
micronota is available under the new BSD license. See COPYING.txt for micronota’s license, and the licenses directory for the licenses of third-party software and databasese that are (either partially or entirely) distributed with micronota.