Cargando…

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

BACKGROUND: Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the k...

Descripción completa

Detalles Bibliográficos
Autores principales:	Yue, Yi, Huang, Hao, Qi, Zhao, Dou, Hui-Min, Liu, Xin-Yi, Han, Tian-Fei, Chen, Yue, Song, Xiang-Jun, Zhang, You-Hua, Tu, Jian
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2020
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7469296/ https://www.ncbi.nlm.nih.gov/pubmed/32723290 http://dx.doi.org/10.1186/s12859-020-03667-3

Ejemplares similares

Binning long reads in metagenomics datasets using composition and coverage information
por: Wickramarachchi, Anuradha, et al.
Publicado: (2022)

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets
por: Hickl, Oskar, et al.
Publicado: (2022)

Protocol for refining metagenomic binning with BinSPreader
por: Ochkalova, Sofia, et al.
Publicado: (2023)

Evaluation of computational phage detection tools for metagenomic datasets
por: Schackart, Kenneth E., et al.
Publicado: (2023)

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
por: Amgarten, Deyvid, et al.
Publicado: (2018)

Quality control and preprocessing of metagenomic datasets
por: Schmieder, Robert, et al.
Publicado: (2011)

Identification of fungi in shotgun metagenomics datasets
por: Donovan, Paul D., et al.
Publicado: (2018)

Metagenomic binning through low-density hashing
por: Luo, Yunan, et al.
Publicado: (2019)

Metagenomic binning with assembly graph embeddings
por: Lamurias, Andre, et al.
Publicado: (2022)

Improving metagenomic binning results with overlapped bins using assembly graphs
por: Mallawaarachchi, Vijini G., et al.
Publicado: (2021)

Spherical: an iterative workflow for assembling metagenomic datasets
por: Hitch, Thomas C. A., et al.
Publicado: (2018)

gbtools: Interactive Visualization of Metagenome Bins in R
por: Seah, Brandon K. B., et al.
Publicado: (2015)

Adversarial and variational autoencoders improve metagenomic binning
por: Líndez, Pau Piera, et al.
Publicado: (2023)

PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets
por: Tausch, Simon H., et al.
Publicado: (2022)

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
por: Pasolli, Edoardo, et al.
Publicado: (2016)

ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
por: Broeksema, Bertjan, et al.
Publicado: (2017)

The CAMI-score: A Novel Tool derived From CAMI Registry to Predict In-hospital Death among Acute Myocardial Infarction Patients
por: Song, Chenxi, et al.
Publicado: (2018)

COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets
por: Bose, Tungadri, et al.
Publicado: (2015)

ConStrains identifies microbial strains in metagenomic datasets
por: Luo, Chengwei, et al.
Publicado: (2015)

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures
por: Strous, Marc, et al.
Publicado: (2012)

Exploiting topic modeling to boost metagenomic reads binning
por: Zhang, Ruichang, et al.
Publicado: (2015)

MBBC: an efficient approach for metagenomic binning based on clustering
por: Wang, Ying, et al.
Publicado: (2015)

Reads Binning Improves Alignment-Free Metagenome Comparison
por: Song, Kai, et al.
Publicado: (2019)

Metaphor—A workflow for streamlined assembly and binning of metagenomes
por: Salazar, Vinícius W, et al.
Publicado: (2023)

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
por: Laczny, Cedric C, et al.
Publicado: (2015)

Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets
por: Li, Weizhong, et al.
Publicado: (2008)

Coverage evaluation of universal bacterial primers using the metagenomic datasets
por: Mao, Dan-Ping, et al.
Publicado: (2012)

Recovering complete and draft population genomes from metagenome datasets
por: Sangwan, Naseer, et al.
Publicado: (2016)

Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting
por: Albanese, Davide, et al.
Publicado: (2015)

Machine Learning for detection of viral sequences in human metagenomic datasets
por: Bzhalava, Zurab, et al.
Publicado: (2018)

Simulating metagenomic stable isotope probing datasets with MetaSIPSim
por: Barnett, Samuel E., et al.
Publicado: (2020)

Soil metagenome datasets underneath the Arecibo Observatory reflector dish
por: Rodriguez-Reyes, Miguel G., et al.
Publicado: (2019)

BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies
por: Chandrakumar, Induja, et al.
Publicado: (2022)

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus
por: Schulz, Frederik, et al.
Publicado: (2020)

Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins
por: Muralidharan, Harihara Subrahmaniam, et al.
Publicado: (2021)

Genome binning of viral entities from bulk metagenomics data
por: Johansen, Joachim, et al.
Publicado: (2022)

vRhyme enables binning of viral genomes from metagenomes
por: Kieft, Kristopher, et al.
Publicado: (2022)

Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools
por: Rotimi, Adeola M., et al.
Publicado: (2018)

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
por: Du, Yuxuan, et al.
Publicado: (2022)

Benchmark dataset and instance generator for real-world three-dimensional bin packing problems
por: Osaba, Eneko, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_50t14edjg5pthvb1q48k56bl1o