https://github.com/biocore/micronota

annotation pipeline for microbial genomes and metagenomes

https://github.com/biocore/micronota

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annotation pipeline for microbial genomes and metagenomes

README.org

#+TITLE: micronota

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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:
  #+BEGIN_SRC sh
    conda install micronota
  #+END_SRC
** install via pip
   You can install through ~pip~:
  #+BEGIN_SRC sh
    pip install micronota
  #+END_SRC

  To install or update to the latest developping version:
  #+BEGIN_SRC
    pip install git+git://github.com/biocore/micronota.git
  #+END_SRC

  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:
  #+BEGIN_SRC
    conda install --file https://raw.githubusercontent.com/biocore/micronota/master/ci/conda_requirements.txt
  #+END_SRC

* 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:
   #+BEGIN_SRC sh
     micronota -h
   #+END_SRC
** To run the default annotation pipeline:
   #+BEGIN_SRC sh
     micronota annotate -i  -o  --out-fmt genbank --kingdom bacteria
   #+END_SRC
** Customize the annotaton:
   You can set up what annotation to run with what parameters by providing a config file when running annotation:
   #+BEGIN_SRC sh
     micronota annotate -i  -o  --out-fmt genbank --kingdom bacteria --config 
   #+END_SRC

   You can modify the [[https://github.com/biocore/micronota/blob/master/micronota/bacteria.yaml][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 [[https://github.com/biocore/micronota/blob/master/CONTRIBUTING.md][CONTRIBUTING.md]].

  See the list of [[https://github.com/biocore/micronota/graphs/contributors][micronota's contributors]].

* Licensing

  micronota is available under the new BSD license. See [[https://github.com/biocore/micronota/blob/master/COPYING.txt][COPYING.txt]] for micronota's license, and [[https://github.com/biocore/micronota/tree/master/licenses][the licenses directory]] for the licenses of third-party software and databasese that are (either partially or entirely) distributed with micronota.

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