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 …

A practical guide to amplicon and metagenomic analysis of microbiome data

YX Liu, Y Qin, T Chen, M Lu, X Qian, X Guo… - Protein & cell, 2021 - academic.oup.com
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …

[HTML][HTML] Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp

X Dong, M Kleiner, CE Sharp, E Thorson, C Li… - Frontiers in …, 2017 - frontiersin.org
Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently
has many applications in microbial ecology. The low costs of the parallel sequencing of …

Current challenges and best-practice protocols for microbiome analysis

R Bharti, DG Grimm - Briefings in bioinformatics, 2021 - academic.oup.com
Analyzing the microbiome of diverse species and environments using next-generation
sequencing techniques has significantly enhanced our understanding on metabolic …

Microbiome helper: a custom and streamlined workflow for microbiome research

AM Comeau, GM Douglas, MGI Langille - MSystems, 2017 - Am Soc Microbiol
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing
and metagenomics, are uncovering associations between microbial taxa and a myriad of …

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

R Ranjan, A Rani, A Metwally, HS McGee… - … and biophysical research …, 2016 - Elsevier
The human microbiome has emerged as a major player in regulating human health and
disease. Translational studies of the microbiome have the potential to indicate clinical …

[HTML][HTML] MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data

DH Huson, S Beier, I Flade, A Górska… - PLoS computational …, 2016 - journals.plos.org
There is increasing interest in employing shotgun sequencing, rather than amplicon
sequencing, to analyze microbiome samples. Typical projects may involve hundreds of …

[HTML][HTML] Advances and challenges in metatranscriptomic analysis

M Shakya, CC Lo, PSG Chain - Frontiers in genetics, 2019 - frontiersin.org
Sequencing-based analyses of microbiomes have traditionally focused on addressing the
question of community membership and profiling taxonomic abundance through amplicon …

[HTML][HTML] Characterization of the gut microbiome using 16S or shotgun metagenomics

J Jovel, J Patterson, W Wang, N Hotte… - Frontiers in …, 2016 - frontiersin.org
The advent of next generation sequencing (NGS) has enabled investigations of the gut
microbiome with unprecedented resolution and throughput. This has stimulated the …

[HTML][HTML] MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

GV Uritskiy, J DiRuggiero, J Taylor - Microbiome, 2018 - Springer
Background The study of microbiomes using whole-metagenome shotgun sequencing
enables the analysis of uncultivated microbial populations that may have important roles in …