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MetaConClust - Unsupervised Binning of Metagenomics Data Using Consensus Clustering

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Title MetaConClust - Unsupervised Binning of Metagenomics Data Using Consensus Clustering
Not Available
 
Creator Sinha Dipro
Sharma Anu
Mishra Dwijesh Chandra
Rai Anil
Lal Shashi Bhushan
Kumar Sanjeev
Farooqi Md. Samir
K. K. Chaturvedi
 
Subject Binning;
PAM;
consensus clustering;
coverage;
metagenomics;
unsupervised clustering
 
Description Not Available
Background: Binning of metagenomic reads is an active area of research, and many unsupervised machine learning-based techniques have been used for taxonomic independent binning of metagenomic reads.

Objective: It is important to find the optimum number of the cluster as well as develop an efficient pipeline for deciphering the complexity of the microbial genome.

Methods: Applying unsupervised clustering techniques for binning requires finding the optimal number of clusters beforehand and is observed to be a difficult task. This paper describes a novel method, MetaConClust, using coverage information for grouping of contigs and automatically finding the optimal number of clusters for binning of metagenomics data using a consensus-based clustering approach. The coverage of contigs in a metagenomics sample has been observed to be directly proportional to the abundance of species in the sample and is used for grouping of data in the first phase by MetaConClust. The Partitioning Around Medoid (PAM) method is used for clustering in the second phase for generating bins with the initial number of clusters determined automatically through a consensus- based method.

Results: Finally, the quality of the obtained bins is tested using silhouette index, rand Index, recall, precision, and accuracy. Performance of MetaConClust is compared with recent methods and tools using benchmarked low complexity simulated and real metagenomic datasets and is found better for unsupervised and comparable for hybrid methods.
Not Available
 
Date 2023-02-28T10:50:41Z
2023-02-28T10:50:41Z
2022-04-29
 
Type Research Paper
 
Identifier Not Available
Not Available
http://krishi.icar.gov.in/jspui/handle/123456789/76502
 
Language English
 
Relation Not Available;
 
Publisher Not Available