Long-read metagenomicsWochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic...
(ABS) of bacterial or fungal ribosomal DNA is the most widely used technology due to its low cost, it suffers from PCR amplification biases that hinder accurate representation of microbial population structures. Shotgun metagenomics (SMG) conversely allows unbiased microbiome profiling but requires ...
Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) to perturb laboratory freshwater mesocosms, simulating sewage contamination events, and followed these mesocosms with shotgun metagenomics over a 7-day observational period. We describe 15 abundant non-...
Big data biology-based predictive models for metagenomics binning Metagenomics is the study of microorganisms collected directly from natural environments using whole genome shotgun (WGS) sequencing. Metagenomics methods ... H Saghir - 《Dissertations & Theses Gradworks》 被引量: 0发表: 2015年 Big da...
Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification progra... P Menzel,KL Ng,A Krogh - 《Nature Communications》 被引量...
Results: In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a ...
Metagenomics can inform questions of virulence,ARGs, and source attribution. Abstract Little is known about the genomic diversity of the microbial communities associated with raw municipal wastewater (sewage), including whether microbial populations specific to sewage exist and how such populations could be...
Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates. We have ...
The genome-integrated perturbagen cassettes are create amplicons which are pooled and sequences determined. This method can be applied to other genome-level single-cell applications - immune receptor profiling, targeted DNA/RNA sequencing, and metagenomics.LABAER, JOSHUAPARK, JIN...
MetagenomicsGRAMMy is a rigorous probabilistic framework for accurately and efficiently estimating Genome Relative Abundance (GRA) based on shotgun metagenomic reads. Users have a wide choice of mapping and alignment tools to assign reads to references. The method is particularly suitable for NGS short...