An introduction to the analysis of shotgun metagenomic data

TJ Sharpton - Frontiers in plant science, 2014 - frontiersin.org
Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms
and clarified the relationship between host-associated microbial communities and host …

Metagenomic data assembly–the way of decoding unknown microorganisms

AL Lapidus, AI Korobeynikov - Frontiers in Microbiology, 2021 - frontiersin.org
Metagenomics is a segment of conventional microbial genomics dedicated to the
sequencing and analysis of combined genomic DNA of entire environmental samples. The …

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 …

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

YW Wu, YH Tang, SG Tringe, BA Simmons, SW Singer - Microbiome, 2014 - Springer
Background Recovering individual genomes from metagenomic datasets allows access to
uncultivated microbial populations that may have important roles in natural and engineered …

New approaches for metagenome assembly with short reads

M Ayling, MD Clark, RM Leggett - Briefings in bioinformatics, 2020 - academic.oup.com
In 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 …

Sequence assembly demystified

N Nagarajan, M Pop - Nature Reviews Genetics, 2013 - nature.com
Advances in sequencing technologies and increased access to sequencing services have
led to renewed interest in sequence and genome assembly. Concurrently, new applications …

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

T Namiki, T Hachiya, H Tanaka… - Proceedings of the 2nd …, 2011 - dl.acm.org
Motivation: An important step of" metagenomics" analysis is the assembly of multiple
genomes from mixed sequence reads of multiple species in a microbial community. Most …

Ray Meta: scalable de novo metagenome assembly and profiling

S Boisvert, F Raymond, É Godzaridis, F Laviolette… - Genome biology, 2012 - Springer
Abstracta Voluminous parallel sequencing datasets, especially metagenomic experiments,
require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a …

High throughput sequencing methods and analysis for microbiome research

JM Di Bella, Y Bao, GB Gloor, JP Burton… - Journal of microbiological …, 2013 - Elsevier
High-throughput sequencing technology is rapidly improving in quality, speed and cost. It is
therefore becoming more widely used to study whole communities of prokaryotes in many …

Computational meta'omics for microbial community studies

N Segata, D Boernigen, TL Tickle… - Molecular systems …, 2013 - embopress.org
Complex microbial communities are an integral part of the Earth's ecosystem and of our
bodies in health and disease. In the last two decades, culture‐independent approaches …