Results 11 to 20 of about 30,341 (174)

DOE JGI Metagenome Workflow [PDF]

mSystems, 2021
The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs data preprocessing, error correction, assembly, structural and functional annotation, and binning.
Alicia Clum, Marcel Huntemann, Brian Bushnell, Brian Foster, Bryce Foster, Simon Roux, Patrick P. Hajek, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Yuko Yoshinaga, Ronan O’Malley, Rekha Seshadri, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh, I-Min A. Chen, Alex Copeland, Natalia N. Ivanova   +18 more
doaj   +2 more sources

Binning sequences using very sparse labels within a metagenome [PDF]

BMC Bioinformatics, 2008
Background In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups.
Halgamuge Saman K, Hsu Arthur L, Chan Chon-Kit, Tang Sen-Lin   +3 more
doaj   +2 more sources

Protocol for refining metagenomic binning with BinSPreader

STAR Protocols, 2023
Summary: The analysis of metagenomic data obtained via high-throughput DNA sequencing is primarily carried out by a dedicated binning process involving clustering contigs, presumably belonging to the same species.
Sofia Ochkalova, Ivan Tolstoganov, Alla Lapidus, Anton Korobeynikov   +3 more
doaj   +2 more sources

The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments [PDF]

BMC Genomics, 2009
Background The characterisation, or binning, of metagenome fragments is an important first step to further downstream analysis of microbial consortia. Here, we propose a one-dimensional signature, OFDEG, derived from the oligonucleotide frequency profile
Halgamuge Saman K, Saeed Isaam
doaj   +2 more sources

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes

BMC Genomics, 2017
Background Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential.
Bhavya Papudeshi, J. Matthew Haggerty, Michael Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano Thompson, Robert A. Edwards, Elizabeth A. Dinsdale   +11 more
doaj   +2 more sources

BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis [PDF]

Nature Communications
Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs).
Zhiguang Qiu, Li Yuan, Chun-Ang Lian, Bin Lin, Jie Chen, Rong Mu, Xuejiao Qiao, Liyu Zhang, Zheng Xu, Lu Fan, Yunzeng Zhang, Shanquan Wang, Junyi Li, Huiluo Cao, Bing Li, Baowei Chen, Chi Song, Yongxin Liu, Lili Shi, Yonghong Tian, Jinren Ni, Tong Zhang, Jizhong Zhou, Wei-Qin Zhuang, Ke Yu   +24 more
doaj   +2 more sources

Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea

Scientific Data, 2022
Measurement(s) metagenome assembled genomes Technology Type(s) metagenome sequencing and genome binning Sample Characteristic - Organism microorganism Sample Characteristic - Environment marine cold seep biome Sample Characteristic - Location South China
Huan Zhang, Minxiao Wang, Hao Wang, Hao Chen, Lei Cao, Zhaoshan Zhong, Chao Lian, Li Zhou, Chaolun Li   +8 more
doaj   +1 more source

Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking

BMC Genomics, 2022
Background So far, a lot of binning approaches have been intensively developed for untangling metagenome-assembled genomes (MAGs) and evaluated by two main strategies.
Ziyao Wu, Yuxiao Wang, Jiaqi Zeng, Yizhuang Zhou   +3 more
doaj   +1 more source

Clustering Fragments Metagenome Using Self-Organizing Map [PDF]

, 2015
Metagenome is a combination of several microorganisms collected from the environment. In metagenome analysis, it is required binning for grouping metagenome fragment yielded by sequencer.
Achmad, Yunita Fauzia, Kusuma, Wisnu Ananta, Sukoco, Heru   +2 more
core   +3 more sources

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC.

PLoS ONE, 2021
Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data.
Bruce Parrello, Rory Butler, Philippe Chlenski, Gordon D Pusch, Ross Overbeek   +4 more
doaj   +1 more source