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Project: nbitk
Version: 0.4.0
Filename: nbitk-0.4.0-py3-none-any.whl
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Uploaded: 2025-02-03 17:57:33 +0000

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Metadata-Version: 2.2
Name: nbitk
Version: 0.4.0
Summary: Naturalis BioInformatics ToolKit
Author-Email: Pierre-Etienne Cholley <pierreetienne.cholley[at]naturalis.nl>, Dick Groenenberg <dick.groenenberg[at]naturalis.nl>, Edwin den Haas <edwin.denhaas[at]naturalis.nl>, Dominika Kresa <dominika.kresa[at]naturalis.nl>, Luka Lenaroto <luka.lenaroto[at]naturalis.nl>, Rutger Vos <rutger.vos[at]naturalis.nl>
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Requires-Dist: biopython
Requires-Dist: pandas
Requires-Dist: openpyxl
Requires-Dist: ete3
Requires-Dist: requests
Requires-Dist: minio
Requires-Dist: pyyaml
Requires-Dist: cutadapt
Requires-Dist: bioblend
Description-Content-Type: text/markdown
License-File: LICENSE
[Description omitted; length: 3681 characters]

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top_level.txt

nbitk
tests