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Tools to help choosing a reference assembly.

Project description

https://img.shields.io/pypi/v/refchooser.svg

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.

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.

Project details


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Files for refchooser, version 0.2.1
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