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Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics ana...
Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provid...
Human papillomavirus (HPV) infection remains a major health threat in sub-Saharan Africa (SSA). HPV self-sampling could help find and treat cervical cancer at an early stage. We aimed to evaluate the effective...
Taxonomic assignment is a crucial step in a metagenomic project which aims to identify the origin of sequences in an environmental sample. Among the existing methods, since composition-based algorithms are not...
In metagenomic sequence data, majority of sequences/reads originate from new or partially characterized genomes, the corresponding sequences of which are absent in existing reference databases. Since taxonomic...
This article is part of a Supplement: Volume 11 Supplement 7
Methane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation ...
A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics). Several different methods have been propos...
Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-ba...
This article is part of a Supplement: Volume 12 Supplement 3
Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-g...
This article is part of a Supplement: Volume 14 Supplement 5
One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classif...
The Correction to this article has been published in Genome Biology 2019 20:72
Metagenomics is the study of environmental samples using sequencing. Rapid advances in sequencing technology are fueling a vast increase in the number and scope of metagenomics projects. Most metagenome sequen...
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 15 Supplement 2
The Correction to this article has been published in Addiction Science & Clinical Practice 2021 16:14
Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial a...
This article is part of a Supplement: Volume 19 Supplement 8
Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads...
The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of m...
Metagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet com...
DNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here...
Biogas is a renewable energy carrier which is used for heat and power production or, in the form of purified methane, as a vehicle fuel. The formation of methane from organic materials is carried out by a mixe...
A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to ...
This article is part of a Supplement: Volume 12 Supplement 2
Metagenomics seeks to understand microbial communities and assemblages by DNA sequencing. Technological advances in next generation sequencing technologies are fuelling a rapid growth in the number and scope o...
This article is part of a Supplement: Volume 14 Supplement 5