Results 1 to 10 of about 6,603 (135)

Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning [PDF]

PeerJ, 2023
Metagenome binning is a key step, downstream of metagenome assembly, to group scaffolds by their genome of origin. Although accurate binning has been achieved on datasets containing multiple samples from the same community, the completeness of binning is
Harrison Ho, Mansi Chovatia, Rob Egan, Guifen He, Yuko Yoshinaga, Ivan Liachko, Ronan O’Malley, Zhong Wang   +7 more
doaj   +3 more sources

Deployable high-fidelity metagenome binning at scale with QuickBin [PDF]

Communications Biology
Reconstructing genomes from metagenomic assemblies is foundational to microbiome research, yet binning faces a persistent trade-off between fidelity and throughput.
Brian Bushnell, Juan C. Villada
doaj   +2 more sources

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery [PDF]

Nature Communications
Metagenomic binning is essential for reconstructing prokaryotic genomes from metagenomic samples. We benchmarked various binning tools using Critical Assessment of Metagenome Interpretation (CAMI)-simulated, custom-simulated, and real metagenomic ...
Jungyeon Kim, Nayeon Kim, Jun Hyung Cha, Junyeong Ma, Insuk Lee   +4 more
doaj   +2 more sources

Reads Binning Improves Alignment-Free Metagenome Comparison

Frontiers in Genetics, 2019
Comparing metagenomic samples is a critical step in understanding the relationships among microbial communities. Recently, next-generation sequencing (NGS) technologies have produced a massive amount of short reads data for microbial communities from ...
Fengzhu Sun, Jie Ren
exaly   +3 more sources

TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive [PDF]

Nature Communications
Metagenomic shotgun sequencing data from over 600,000 metagenomes are publicly available in repositories such as NCBI’s Sequence Read Archive (SRA).
Eike Matthias Wacker, Malte Christoph Rühlemann, Andre Franke, David Ellinghaus   +3 more
doaj   +2 more sources

SolidBin: improving metagenome binning with semi-supervised normalized cut [PDF]

Bioinformatics, 2019
Shanfeng Zhu, Fengzhu Sun, Ziye Wang
exaly   +2 more sources

Evaluation of metagenome binning: advances and challenges [PDF]

Briefings in Bioinformatics
Söding Soeding Söding
exaly   +2 more sources

BinSPreader: Refine binning results for fuller MAG reconstruction

iScience, 2022
Summary: Despite the recent advances in high-throughput sequencing, metagenome analysis of microbial populations still remains a challenge. In particular, the metagenome-assembled genomes (MAGs) are often fragmented due to interspecies repeats, uneven ...
Ivan Tolstoganov, Yuri Kamenev, Roman Kruglikov, Sofia Ochkalova, Anton Korobeynikov   +4 more
doaj   +1 more source

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies [PDF]

PeerJ, 2019
We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species.
Dongwan D. Kang, Feng Li, Edward Kirton, Ashleigh Thomas, Rob Egan, Hong An, Zhong Wang   +6 more
doaj   +2 more sources

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities [PDF]

PeerJ, 2015
Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions.
Dongwan D. Kang, Jeff Froula, Rob Egan, Zhong Wang   +3 more
doaj   +2 more sources