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Metagenomic Data Analysis
This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control...
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cgMSI: pathogen detection within species from nanopore metagenomic sequencing data
BackgroundMetagenomic sequencing is an unbiased approach that can potentially detect all the known and unidentified strains in pathogen detection....
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Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons
Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the...
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In Silico Analysis of Phylogeny, Structure, and Function of Flavohemoproteins from Metagenomic Data
AbstractIn this study, flavohemoproteins from protist, bacterial and fungal sources as well those available in metagenome data have been...
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Precision enzyme discovery through targeted mining of metagenomic data
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes...
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Metagenomic data highlight shifted nitrogen regime induced by wetland reclamation
Natural wetlands are mostly nitrogen-limited ecosystems, while reclamation stimulates the loss of nitrogen (N) in soils by shifting the N regime. To...
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Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE
BackgroundThe human microbiome plays a critical role in maintaining human health. Due to the recent advances in high-throughput sequencing...
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Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
BackgroundAs most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data...
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Adversarial and variational autoencoders improve metagenomic binning
Assembly of reads from metagenomic samples is a hard problem, often resulting in highly fragmented genome assemblies. Metagenomic binning allows us...
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Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis
Early detection of human disease is associated with improved clinical outcomes. However, many diseases are often detected at an advanced, symptomatic...
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Cont-ID: detection of sample cross-contamination in viral metagenomic data
BackgroundHigh-throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important...
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Toward efficient and high-fidelity metagenomic data from sub-nanogram DNA: evaluation of library preparation and decontamination methods
BackgroundShotgun metagenomic sequencing has greatly expanded the understanding of microbial communities in various biological niches. However, it is...
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MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data
BackgroundThe importance of the human microbiome in the analysis of various diseases is emerging. The two main methods used to profile the human...
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aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow
Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles,...
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Recent Advances in Metagenomic Approaches, Applications, and Challenges
Advances in metagenomics analysis with the advent of next-generation sequencing have extended our knowledge of microbial communities as compared to...
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Integration of polygenic and gut metagenomic risk prediction for common diseases
Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective...
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Fast and robust metagenomic sequence comparison through sparse chaining with skani
Sequence comparison tools for metagenome-assembled genomes (MAGs) struggle with high-volume or low-quality data. We present skani (
https://github.com/bluenote-1577/skani... 
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Mora: abundance aware metagenomic read re-assignment for disentangling similar strains
BackgroundTaxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but...
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Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing
The plant microbiome is crucial for plant growth, yet many important questions remain, such as the identification of specific bacterial species in...
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Recent Trends in Metagenomic Approaches in Environmental Cleanup
Metagenomic approaches are being widely used to detect all culturable and unculturable microbes present in environmental samples in a time-saving and...