Results 11 to 20 of about 138,246 (299)

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

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

The Oral Microbiome of King Richard III of England. [PDF]

Am J Biol Anthropol
ABSTRACT Objectives Metagenomic investigations of ancient dental calculus provide insights into oral health, disease, and diet. Here, we analyze the dental calculus metagenome of King Richard III of England (1452–1485). Materials and Methods Dental calculus DNA was extracted from three teeth of King Richard III and shotgun sequenced to a depth of ...
Velsko IM, Hübner A, Fagernäs Z, Yates JAF, Mann AE, Hofman CA, Ozga AT, Lewis CM, Speller C, Fiddyment S, Francken M, Wahl J, Krause J, Radini A, King T, Warinner C.   +15 more
europepmc   +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

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

metagenome-atlas/atlas: V2.9

, 2022
ATLAS - Three commands to start analyzing your metagenome ...
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

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

Enhanced mitochondrial activity reshapes a gut microbiota profile that delays NASH progression

Hepatology, EarlyView., 2022
Improved mitochondrial activity, due to the lack of methylation‐controlled J protein (MCJ), creates a specific microbiota signature that when transferred through cecal microbiota transplantation delays NASH progression by restoring the gut‐liver axis and enhancing hepatic fatty acid oxidation.
María Juárez‐Fernández, Naroa Goikoetxea‐Usandizaga, David Porras, María Victoria García‐Mediavilla, Miren Bravo, Marina Serrano‐Maciá, Jorge Simón, Teresa C. Delgado, Sofía Lachiondo‐Ortega, Susana Martínez‐Flórez, Óscar Lorenzo, Mercedes Rincón, Marta Varela‐Rey, Leticia Abecia, Héctor Rodríguez, Juan Anguita, Esther Nistal, María Luz Martínez‐Chantar, Sonia Sánchez‐Campos   +18 more
wiley   +1 more source

Clinical metagenomics [PDF]

Nature Reviews Genetics, 2019
Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of ...
Charles Y. Chiu, Steven A. Miller
openaire   +4 more sources

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