Results 11 to 20 of about 140,801 (215)

How much metagenome data is needed for protein structure prediction: The advantages of targeted approach from the ecological and evolutionary perspectives

iMeta, 2022
It has been proven that three‐dimensional protein structures could be modeled by supplementing homologous sequences with metagenome sequences. Even though a large volume of metagenome data is utilized for such purposes, a significant proportion of ...
Pengshuo Yang, Kang Ning
exaly   +2 more sources

MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework [PDF]

Cell Genomics
Summary: Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems but is fraught with technical hurdles. We introduce MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking; https ...
Michal Ziemski, Liz Gehret, Anthony Simard, Santiago Castro Dau, Vinzent Risch, Doriela Grabocka, Christos Matzoros, Colin Wood, Paula Momo Cabrera, Rodrigo Hernández-Velázquez, Milo R. Schärer, Felicia Sandberg, Chloe Herman, Keegan Evans, Michael S. Robeson, II, Evan Bolyen, J. Gregory Caporaso, Nicholas A. Bokulich   +17 more
doaj   +2 more sources

High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly

Frontiers in Microbiology, 2022
Metagenome assembly is a core yet methodologically challenging step for taxonomic classification and functional annotation of a microbiome. This study aims to generate the high-resolution human gut metagenome using both Illumina and Nanopore platforms ...
Ning Dong, Lianwei Ye, Wenguang Xiong
exaly   +3 more sources

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

Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP) based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India

Genomics Data, 2015
Bacterial diversity and archaeal diversity in metagenome of the Lonar soda lake sediment were assessed by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP).
Anjana Ghelani, Pravin Dudhagara, Shreyas Bhatt   +2 more
exaly   +3 more sources

Phage therapy for Clostridioides difficile infection

Frontiers in Immunology, 2022
Clostridioides difficile is endemic in the intestinal tract of healthy people. However, it is responsible for many healthcare-associated infections, such as nosocomial diarrhea following antibiotic treatment.
Kosuke Fujimoto, Kosuke Fujimoto, Satoshi Uematsu, Satoshi Uematsu   +3 more
doaj   +1 more source

Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients. [PDF]

Adv Sci (Weinh)
Based on genome size‐functional breadth theory, we introduce and validate a framework that adjudicates conflicting average genome size (AGS) estimates by testing which estimate yields a gap between scaled functional diversity and scaled taxonomic diversity that is consistent with the expected positive association between genome size and gene functional
Zhu H, Chen X, Li Q, Sun C, Xia H, Huang Y, Wang C, Chen P, Gao C.   +8 more
europepmc   +2 more sources

Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition

mSystems, 2023
Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome.
Kayla A. Carter, Anthony A. Fodor, Jennifer E. Balkus, Angela Zhang, Myrna G. Serrano, Gregory A. Buck, Stephanie M. Engel, Michael C. Wu, Shan Sun   +8 more
doaj   +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   +2 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