Skip to main content

CFIA OLC Genome Quality Assessment with Machine Learning

Project description

[![Build status](](
# GenomeQAML: Genome Quality Assesment with Machine Learning

The GenomeQAML is a script that uses a pre-computed ExtraTreesClassifier model in order to
classify FASTA-formatted _de novo_ assemblies as bad, good, or very good. It's easy to use,
and has minimal dependencies.

## External Dependencies

- [Mash (v2.0 or greater)](
- [Prodigal (>=2.6.2)](

Both of these need to be downloaded and included on your $PATH.

## Installation

All you need to do is install with pip: `pip install genomeqaml`.

Usage of a virtualenv
is highly recommended.

## Usage

GenomeQAML takes a directory containing uncompressed fasta files as input - these will be classified and a
report written to a CSV-formatted file for your inspection.

To run, type ` -t /path/to/fasta/folder`

This will create a report, by default called `QAMLreport.csv`. You can change the name
of the report with the `-r` argument.

usage: [-h] -t TEST_FOLDER [-r REPORT_FILE]

optional arguments:
-h, --help show this help message and exit
-t TEST_FOLDER, --test_folder TEST_FOLDER
Path to folder containing FASTA files you want to
-r REPORT_FILE, --report_file REPORT_FILE
Name of output file. Default is QAMLreport.csv.


Project details

Release history Release notifications

This version
History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
GenomeQAML-0.0.11.tar.gz (8.1 MB) Copy SHA256 hash SHA256 Source None Feb 5, 2018

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page