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An efficient toolkit for constructing and processing taxonomic trees (metagenomic reads count, remapping, etc.).

Project description

living-tree-toolkit

An efficient toolkit for processing taxonomic trees (abundance calculations, reads count statistics, etc.) and generating taxonomic trees using lineages data retrieved from the NCBI taxonomy database.

Status Beta PRs Welcome Read the Docs (version)

Use treelib API to achieve rapid construction of complex trees and ete3 toolkit API to retrieve data from NCBI taxonomy database.

This project is a sub-project of the ONN4MDM project, if you use it for academic purposes, please cite us.

Update

  • 2020/03/27:
    • start finalizing project framework and release initial version.
  • 2020/04/14:
    • Api update update_value and get_matrix
    • New method get_top_down_ids, get_bottom_up_ids, get_ids_by_level and get_paths_to_level
    • Execution efficiency are improved significantly

Documentation

For Installation, examples and API references, see https://living-tree-toolkit.readthedocs.io/en/latest/

Maintainer

Name Email Organization
Hui Chong huichong.me@gmail.com Research Assistant, Institute of Science and Technology for Brain-inspired Intelligence, Fudan University

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