Results 11 to 20 of about 1,283,302 (227)

High-quality metagenome assembly from long accurate reads with metaMDBG [PDF]

Nature Biotechnology
International audienceWe introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome ...
Sébastien Raguideau, Rayan Chikhi, Christopher Quince   +2 more
exaly   +5 more sources

New approaches for metagenome assembly with short reads [PDF]

Briefings in Bioinformatics, 2020
AbstractIn recent years, the use of longer range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic data sets, as assumptions made by the single genome assembly algorithms do not apply when ...
Matthew Clark, Richard M Leggett
exaly   +5 more sources

Spherical: an iterative workflow for assembling metagenomic datasets [PDF]

BMC Bioinformatics, 2018
Background The consensus emerging from the study of microbiomes is that they are far more complex than previously thought, requiring better assemblies and increasingly deeper sequencing.
Thomas C. A. Hitch, Christopher J. Creevey   +1 more
doaj   +7 more sources

Extreme Scale De Novo Metagenome Assembly [PDF]

SC18: International Conference for High Performance Computing, Networking, Storage and Analysis, 2018
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big
Steven Hofmeyr, Georganas, Evangelos, Evangelos Georganas, Katherine Yelick, Arndt, Bill, Hofmeyr, Steven A, Buluç, Aydin, Andrew Tritt, Leonid Oliker, Hofmeyr, Steven, Bill Arndt, Eugene Goltsman, Rob Egan, Aydin Buluc, Tritt, Andrew, Egan, Rob, Goltsman, Eugene, Yelick, Katherine A, Yelick, Katherine, Hofrneyr, Steven, Oliker, Leonid   +20 more
core   +10 more sources

Benchmarking different approaches for Norovirus genome assembly in metagenome samples

BMC Genomics, 2021
Background Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains ...
Azahara Fuentes-Trillo, Carolina Monzó, Iris Manzano, Cristina Santiso-Bellón, Juliana da Silva Ribeiro de Andrade, Roberto Gozalbo-Rovira, Ana-Bárbara García-García, Jesús Rodríguez-Díaz, Felipe Javier Chaves   +8 more
doaj   +3 more sources

STRONG: metagenomics strain resolution on assembly graphs [PDF]

Genome Biology, 2021
We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to ...
Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, Orkun S. Soyer, J. Kimberly Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi, Aaron E. Darling   +9 more
doaj   +6 more sources

Metagenome assembly of high-fidelity long reads with hifiasm-meta [PDF]

Nature Methods, 2022
Xiaowen Feng, Haoyu Cheng, Heng Li
exaly   +2 more sources

Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes

Cell Reports Methods
Summary: Generating metagenome-assembled genomes from DNA shotgun sequencing datasets can demand considerable computational resources. Here, we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive ...
Jeffrey Gordon, Hannah M Lynn
exaly   +3 more sources

The chromosomal genome sequence of the lesser starlet coral, Siderastrea radians (Pallas, 1766) (Scleractinia: Rhizangiidae) and its associated microbial metagenome sequences [version 1; peer review: 2 approved] [PDF]

Wellcome Open Research
We present a genome assembly from a specimen of Siderastrea radians (lesser starlet coral; Cnidaria; Anthozoa; Scleractinia; Rhizangiidae). The genome sequence has a total length of 807.19 megabases.
Eerik Aunin, Victoria McKenna, Graeme Oatley, Sebastian Metz, Elizabeth Sinclair, Camilla Santos, Haoyu Niu, Michael Paulini, Michael Sweet, Camile Avelino, Andrew Baker, Richard Karp, Noah Gettle, Rebecca O’Brien   +13 more
doaj   +2 more sources

Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing

Microbiology Spectrum
Oxford Nanopore sequencing is one of the high-throughput sequencing technologies that facilitates the reconstruction of metagenome-assembled genomes (MAGs).
Zhao Chen, Jianghong Meng, Padmini Ramachandran   +2 more
exaly   +3 more sources