Shotgun metagenomics, from sampling to analysis

C Quince, AW Walker, JT Simpson, NJ Loman… - Nature …, 2017 - nature.com
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …

MEGAHIT v1. 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices

D Li, R Luo, CM Liu, CM Leung, HF Ting, K Sadakane… - Methods, 2016 - Elsevier
The study of metagenomics has been much benefited from low-cost and high-throughput
sequencing technologies, yet the tremendous amount of data generated make analysis like …

Deciphering factors driving soil microbial life‐history strategies in restored grasslands

Y Yang, Y Dou, B Wang, Z Xue, Y Wang, S An… - Imeta, 2023 - Wiley Online Library
In macroecology, the concept of r‐and K‐strategy has been widely applied, yet, there have
been limited studies on microbial life‐history strategies in temperate grasslands using …

[HTML][HTML] Strains, functions and dynamics in the expanded Human Microbiome Project

J Lloyd-Price, A Mahurkar, G Rahnavard, J Crabtree… - Nature, 2017 - nature.com
The characterization of baseline microbial and functional diversity in the human microbiome
has enabled studies of microbiome-related disease, diversity, biogeography, and molecular …

metaSPAdes: a new versatile metagenomic assembler

S Nurk, D Meleshko, A Korobeynikov… - Genome …, 2017 - genome.cshlp.org
While metagenomics has emerged as a technology of choice for analyzing bacterial
populations, the assembly of metagenomic data remains challenging, thus stifling biological …

Binning metagenomic contigs by coverage and composition

J Alneberg, BS Bjarnason, I De Bruijn, M Schirmer… - Nature …, 2014 - nature.com
Shotgun sequencing enables the reconstruction of genomes from complex microbial
communities, but because assembly does not reconstruct entire genomes, it is necessary to …

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

C Hahn, L Bachmann, B Chevreux - Nucleic acids research, 2013 - academic.oup.com
We present an in silico approach for the reconstruction of complete mitochondrial genomes
of non-model organisms directly from next-generation sequencing (NGS) data …

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

L Žifčáková, T Větrovský, A Howe… - Environmental …, 2016 - Wiley Online Library
Understanding the ecology of coniferous forests is very important because these
environments represent globally largest carbon sinks. Metatranscriptomics, microbial …

[HTML][HTML] Structure and function of the healthy pre-adolescent pediatric gut microbiome

EB Hollister, K Riehle, RA Luna, EM Weidler… - Microbiome, 2015 - Springer
Background The gut microbiome influences myriad host functions, including nutrient
acquisition, immune modulation, brain development, and behavior. Although human gut …

The present and future of de novo whole-genome assembly

J Sohn, JW Nam - Briefings in bioinformatics, 2018 - academic.oup.com
As the advent of next-generation sequencing (NGS) technology, various de novo assembly
algorithms based on the de Bruijn graph have been developed to construct chromosome …