micronota

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.

Introduction

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.

Install

install via conda

To install the latest release of micronota:

conda install micronota

install via pip

You can install through pip:

pip install micronota

To 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

Prepare Databases

You need to download database files:

Databases	Supported	Download URL
UniRef	yes
Rfam	yes
ResFam	ongoing

Usage

You can see the command supported by micronota with:

micronota -h

To run the default annotation pipeline:

micronota annotate -i <input.fna> -o <output-dir> --out-fmt genbank --kingdom bacteria

Customize the annotaton:

You 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.

Sequence Features to Annotate

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

Contributing

If you’re interested in getting involved in micronota development, see CONTRIBUTING.md.

See the list of micronota’s contributors.

Licensing

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.