gaet 0.3.0

Evaluate the quality of a genome assembly based on annotated genes

Gene-based assembly evaluation tool - evaluate a single assembly or compare two assemblies using their annotations.

Getting Started

pip install [--user] gaet

gaet assembly.gff
gaet --reference reference.gff assembly.gff

Gaet is written in python 3. If you would prefer, there is a precompiled version of gaet which runs on Linux systems.

Documentation

See gaet(1) for a description of how to run gaet. See gaet-format(5) for a description of the output metrics generated by gaet.

Running the tests

Gaet has both unit tests and feature tests. The unit tests check individual python functions within the code. The feature tests are run against the compiled version of gaet and ensure the program works as a whole.

make test
make feature

Upon a successful pull request onto the master branch, where all tests pass, a new version of gaet will be released to pypi, and a new precompiled version released to S3.

Built With

• funcy - functional programming for python

• gffutils - Utilities for accessing GFF data

• pyfaidx - Accessing substrings of FASTA data

• ruamel.yaml - actively maintained YAML parsing for python

Authors

• Michael Barton

License

This project is licensed under the BSD License - see the LICENSE.txt file for details.

See also

• QUAST- check the completeness of an assembly or compare with a reference using size metrics such nga50.

• checkm - checks the completeness of an assembly using the expectation of certain essential genes.