Results 51 to 60 of about 1,283,302 (227)

metagenome assembly using GPUs

, 2021
Metagenomic workflows involve studying uncultured microorganisms directly from the environment. These environmental samples when processed by modern sequencing machines yield large and complex datasets that exceed the capabilities of metagenomic software.
Deslippe, Jack, Steven Hofmeyr, Muaaz Gul Awan, Katherine Yelick, Leonid Oliker, Hofmeyr, Steven, Jack Deslippe, Nan Ding, Buluc, Aydin, Awan, Muaaz Gul, Rob Egan, Aydin Buluc, Egan, Rob, Ding, Nan, Yelick, Katherine, Oliker, Leonid   +15 more
core   +1 more source

Accuracy and Completeness of Long Read Metagenomic Assemblies

Microorganisms, 2022
Microbes influence the surrounding environment and contribute to human health. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy.
Jeremy Buttler, Devin Drown
openaire   +3 more sources

Algorithmic and computational comparison of metagenome assemblers

The Indian Journal of Agricultural Sciences, 2020
Assembly of genome sequences of a microbial community is computationally challenging and complex than its single genome counterparts. Keeping in view the volume, diversity and varied abundance of different microbes, number of metagenome assemblers have ...
ANU SHARMA, DWIJESH CHANDRA MISHRA, NEERAJ BUDHLAKOTI, ANIL RAI, SHASHI BHUSHAN LAL, SANJEEV KUMAR   +5 more
doaj   +1 more source

Shotgun metagenome sequencing and recovery of 444 metagenome-assembled microbial genomes from the biofloc aquaculture system

, 2023
We assembled a total of 444 medium- to high-quality metagenome-assembled genomes (MAGs) with completeness > 50% and contamination < 5%, from floc-associated bacterial community (FAB) of a commercial shrimp biofloc aquaculture system, located in South ...
Yeonjung Lim (6645230), Jang-Cheon Cho (518240), Meora Rajeev (11485592), Ilsuk Jung (16468119), Suhyun Kim (226047), Ilnam Kang (518235)   +5 more
core   +1 more source

Metagenome-assembled-genomes (MAGs)

, 2022
MAGs were constructed using snakemake metagenome workflow in anvi'o (Eren et al., 2015).  A detailed explanation on the workflow (such as the softwares used in anvi'o) can be found in the supplementary material of the paper.
Ömer Coskun (9725927)
core   +1 more source

Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome. [PDF]

Mol Ecol Resour
ABSTRACT Strain‐level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain‐level resolution of individual microbes.
Sahil R, Jain M.
europepmc   +2 more sources

metagenome-atlas/atlas: Bug fixes Drep

, 2021
ATLAS - Three commands to start analyzing your metagenome ...
Silas Kieser, Jackson M. Tsuji, Richard Allen White III, Christopher Bottoms, Joe Brown, Sean M. Colby, Vladimir Mikryukov, wangzc, Chris Overall, Mattias de Hollander, C. Titus Brown, Colin Brislawn   +11 more
core   +1 more source

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS [PDF]

Journal of Bioinformatics and Computational Biology, 2008
Metagenomics is an emerging methodology for the direct genomic analysis of a mixed community of uncultured microorganisms. The current analyses of metagenomics data largely rely on the computational tools originally designed for microbial genomics projects.
Yuzhen Ye, Haixu Tang
openaire   +4 more sources

metagenome-atlas/atlas: GTDB v 207 low memory profiling

, 2022
New Features GTDB version 207 Low memory taxonomic annotation Minor changes Fix Typos by @roshni-b in https://github.com/metagenome-atlas/atlas/pull/520 Speed up DRAM annotations by @jmtsuji in https://github.com/metagenome-atlas/atlas/pull/534 Full ...
Silas Kieser, Richard Allen White III, Joe Brown, Vladimir Mikryukov, Roshni Biswas, 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   +15 more
core   +1 more source

Noncanonical Peloruside A Biosynthesis by an Uncultivated Verrucomicrobiota Symbiont

Angewandte Chemie, EarlyView.
Noncanonical biochemistry of the peloruside PKS characterized in this work, comprising double bond generation by a noncanonical tridomain (blue), acetyl‐CoA recycling (orange), and proofreading systems (purple and yellow). The Z‐double bond is installed by TEB1 through O‐acetylation and acetate elimination. The acyl ligase PelB (AL, orange) selectively
Amy E. Fraley, Michael Rust, Moritz Wagner, Ida R. Hipfinger, Paul J. N. Böhm, Cora L. Dieterich, Christopher M. Field, Michael J. Page, Jeremy G. Owen, Robert A. Keyzers, Shinichi Sunagawa, Jörn Piel   +11 more
wiley   +2 more sources