Metadata-Version: 2.1
Name: recentrifuge
Version: 1.14.1
Summary: Robust comparative analysis and contamination removal for metagenomics
Home-page: http://www.recentrifuge.org
Author: Jose Manuel Martí
Author-email: jse.mnl@gmail.com
License: AGPL except krona.js, with its own license by BNBI
Project-URL: Documentation, https://github.com/khyox/recentrifuge/wiki
Project-URL: Source, https://github.com/khyox/recentrifuge
Project-URL: Tracker, https://github.com/khyox/recentrifuge/issues
Keywords: metagenomics comparative-analysis contamination-removal
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: JavaScript
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: biopython (==1.79)
Requires-Dist: numpy (>=1.19.5)
Requires-Dist: openpyxl (==3.1.2)
Requires-Dist: matplotlib (>=3.3.4)
Requires-Dist: pandas (<2.0.0)


**Robust comparative analysis and contamination removal for metagenomics**

[![Retest](https://github.com/khyox/Recentrifuge/actions/workflows/retest.yaml/badge.svg?branch=v1.14.1)](https://github.com/khyox/recentrifuge/actions/workflows/retest.yaml)

With Recentrifuge, researchers can interactively explore what organisms are in their samples and at which level of confidence, thus enabling a robust comparative analysis of multiple samples in any metagenomic study.

 * Removes diverse contaminants, including crossovers, using a novel **robust contamination removal** algorithm.
 * Provides a **confidence level for every result**, since the calculated score propagates to all the downstream analysis and comparisons.
 * Unveils the generalities and specificities in the metagenomic samples, thanks to a new **comparative analysis engine**.

Recentrifuge's novel approach combines robust statistics, arithmetic of scored taxonomic trees, and parallel computational algorithms.

Recentrifuge is especially useful when a more **reliable detection of minority organisms** is needed (e.g. in the case of low microbial biomass metagenomic studies) in clinical, environmental, or forensic analysis. Beyond the standard confidence levels, Recentrifuge implements others devoted to variable length reads, very convenient for complex datasets generated by **nanopore sequencers**.

____

To play with an example of a webpage generated by Recentrifuge, click on the next screenshot: 

<p align="center">
  <a href="https://rawgit.com/khyox/rcf-aux/master/TEST.rcf.html?dataset=5&node=0&collapse=false&color=true&depth=30&font=12&key=true" target="_blank">
    <img src="https://raw.githubusercontent.com/khyox/rcf-aux/master/RCF_screenshot_750.png" alt="Recentrifuge test screenshot" width="750px"/></a></p>
<p align="center">
  <a href="https://rawgit.com/khyox/rcf-aux/master/TEST.rcf.html?dataset=5&node=0&collapse=false&color=true&depth=30&font=12&key=true" target="_blank">Recentrifuge webpage example</a><p align="center">


