Results 31 to 40 of about 1,283,302 (227)

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

BMC Bioinformatics, 2021
Background Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in
Zachary Deng, Eric Delwart
doaj   +1 more source

metaSPAdes: a new versatile metagenomic assembler [PDF]

Genome Research, 2017
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of ...
Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A. Pevzner   +3 more
openaire   +2 more sources

Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling

Frontiers in Microbiology, 2022
The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years.
Mindia A. S. Haryono, Ying Yu Law, Krithika Arumugam, Larry C. -W. Liew, Thi Quynh Ngoc Nguyen, Daniela I. Drautz-Moses, Stephan C. Schuster, Stephan C. Schuster, Stefan Wuertz, Stefan Wuertz, Rohan B. H. Williams   +10 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

metagenome-atlas/atlas: v2.12.0

, 2022
What's Changed GTDB-tk requires rule extract_gtdb to run first by @Waschina in https://github.com/metagenome-atlas/atlas/pull/551 use Galah instead of Drep use bbsplit for mapping to genomes (maybe move to minimap in future) faster gene catalogs ...
Silas Kieser, Richard Allen White III, Joe Brown, Vladimir Mikryukov, Roshni Biswas, Yan Hui, Jackson M. Tsuji, Christopher Bottoms, Silvio Waschina, Cedric Midoux, Jie Zhu, Sean M. Colby, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +16 more
core   +1 more source

Evaluation of short read metagenomic assembly [PDF]

2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2010
Metagenomic assembly is a challenging problem due to the presence of genetic material from multiple organisms. The problem becomes even more difficult when short reads produced by next generation sequencing technologies are used. Although whole genome assemblers are not designed to assemble metagenomic samples, they are being used for metagenomics due ...
Anveshi Charuvaka, Huzefa Rangwala
openaire   +4 more sources

SCAPP: an algorithm for improved plasmid assembly in metagenomes [PDF]

Microbiome, 2020
Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance.
David Pellow, Alvah Zorea, Maraike Probst, Ori Furman, Arik Segal, Itzhak Mizrahi, Ron Shamir   +6 more
openaire   +4 more sources

metagenome-atlas/atlas: v2.9.0

, 2022
What's Changed Start an atlas project from public data in SRA Docs Make atlas ready for python 3.10 https://github.com/metagenome-atlas/atlas/pull/498 Add strain profiling using inStrain You can run atlas run genomes strains New Contributors @alienzj
Silas Kieser, Richard Allen White III, Joe Brown, Vladimir Mikryukov, Yan Hui, Jackson M. Tsuji, Christopher Bottoms, Cedric Midoux, Jie Zhu, Sean M. Colby, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +14 more
core   +1 more source

Assembly of viral genomes from metagenomes [PDF]

Frontiers in Microbiology, 2014
Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses.
Saskia L Smits, Saskia L Smits, Rogier eBodewes, Aritz eRuiz-Gonzalez, Aritz eRuiz-Gonzalez, Aritz eRuiz-Gonzalez, Wolfgang eBaumgärtner, Marion P Koopmans, Marion P Koopmans, Albert D. M. E Osterhaus, Albert D. M. E Osterhaus, Anita C Schürch   +11 more
openaire   +5 more sources

Strainberry: automated strain separation in low-complexity metagenomes using long reads

Nature Communications, 2021
Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and ...
Riccardo Vicedomini, Christopher Quince, Aaron E. Darling, Rayan Chikhi   +3 more
doaj   +1 more source