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Tools to help choosing a reference assembly.

Project description

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.


  • 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:


See the LICENSE file included in the refchooser distribution.


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.

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refchooser-0.2.1.tar.gz (22.8 kB view hashes)

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