refchooser 0.2.1

Tools to help choosing a reference assembly.

Tools to help choose a reference from a list of assemblies.

The refchooser project was developed by the United States Food and Drug Administration, Center for Food Safety and Applied Nutrition.

• Free software
• Documentation: https://refchooser.readthedocs.io
• Source Code: https://github.com/CFSAN-Biostatistics/refchooser
• PyPI Distribution: https://pypi.python.org/pypi/refchooser

Features

• Print a table of metrics to help choose an assembly from a collection.
• N50
• N90
• Number of contigs
• Assembly length
• Mean mash distance to all other assemblies

Citing refchooser

To cite refchooser, please reference the refchooser GitHub repository:

https://github.com/CFSAN-Biostatistics/refchooser

License

See the LICENSE file included in the refchooser distribution.

History

0.2.1 (2019-08-20)

• Detect and exclude empty assemblies.

0.2.0 (2019-07-12)

• Add N50 and N90 metrics.
• Calculate a simple “Score” for each assembly, the N50/Distance ratio.
• Combine all metrics in a single table sortable by any column.

0.1.0 (2019-06-21)

• Initial version.