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
- Print a table of metrics to help choose an assembly from a collection.
- Number of contigs
- Assembly length
- Mean mash distance to all other assemblies
To cite refchooser, please reference the refchooser GitHub repository:
See the LICENSE file included in the refchooser distribution.
- Detect and exclude empty assemblies.
- 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.
- Initial version.
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