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guitools

Generates taxonomic abundance from bracken report file

https://github.com/gmoreiravet/guitools

Science Score: 44.0%

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Repository

Generates taxonomic abundance from bracken report file

Basic Info
  • Host: GitHub
  • Owner: GmoreiraVet
  • Language: Python
  • Default Branch: main
  • Size: 77.1 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Created over 1 year ago · Last pushed 11 months ago
Metadata Files
Readme Citation

README.md

Guitools

Guitools is a Python-based toolkit designed to process Bracken output files and generate comprehensive taxonomic abundance visualizations. It supports various analyses, including heatmaps, dendrograms, stacked bar plots, beta diversity (PCoA), bubble graphs, and rarefaction curve analyses. This makes it ideal for microbial ecology and metagenomics studies.

Features

  • Heatmaps: Taxonomic abundance across samples.
  • Dendrograms: Sample clustering based on Bray-Curtis dissimilarity.
  • Stacked Bar Plots: Visualize relative abundance across taxonomic groups.
  • Beta Diversity (PCoA): Bray-Curtis dissimilarity for visualizing compositional differences (2 and 3 axis).
  • Bubble Graphs: Compare taxa abundances.
  • Rarefaction Curves: Assess alpha diversity based on sequencing depth.

Installation

Prerequisites

  • Python 3.8 or higher
  • Required libraries: pandas, glob, os, plotly, matplotlib, seaborn, scipy, skbio

Install dependencies:

bash pip install pandas plotly matplotlib seaborn scipy scikit-bio Clone the Repository bash git clone https://github.com/GmoreiraVet/Guitools.git cd Guitools

Usage

Preparing Input Files Input Folder: Place Bracken report files in the designated directory. Default path: python input_folder = "/home/viroicbas/scriptTeste/bracken_reports/" Modify inputfolder in the scripts if needed. File Naming: Ensure Bracken report files follow the naming format SAMPLEbracken.txt

(Most Scripts now ask the user for the file path instead)

Outputs

Each script saves visualizations as HTML or PNG files in the working directory, ready for publication.

:books: Citation :books:

If you use Guitools in your research, please consider citing the software. You can generate the citation directly from GitHub by using the "Cite this repository" button located in the repository's header (next to the "Fork" and "Star" buttons). This will generate a citation formatted in the recommended style for GitHub repositories.

Thank you for your support!

Owner

  • Login: GmoreiraVet
  • Kind: user

Citation (citation.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "Guitools"
authors:
  - family-names: "Moreira"
    given-names: "Guilherme"
    orcid: "https://orcid.org/0009-0002-2828-7202
date-released: "2025-02-13" 
version: "1.1.1" 
repository-code: "https://github.com/GmoreiraVet/Guitools"
doi: https://doi.org/10.5281/zenodo.14870717

GitHub Events

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Last Year
  • Release event: 3
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  • Push event: 26
  • Create event: 3