Virtifier: a deep learning-based identifier for viral sequences from metagenomes
Y Miao, F Liu, T Hou, Y Liu - Bioinformatics, 2022 - academic.oup.com
Motivation Viruses, the most abundant biological entities on earth, are important
components of microbial communities, and as major human pathogens, they are …
components of microbial communities, and as major human pathogens, they are …
RNN-VirSeeker: a deep learning method for identification of short viral sequences from metagenomes
F Liu, Y Miao, Y Liu, T Hou - IEEE/ACM Transactions on …, 2020 - ieeexplore.ieee.org
Viruses are the most abundant biological entities on earth, and play vital roles in many
aspects of microbial communities. As major human pathogens, viruses have caused huge …
aspects of microbial communities. As major human pathogens, viruses have caused huge …
[HTML][HTML] Assembly of viral genomes from metagenomes
SL Smits, R Bodewes, A Ruiz-Gonzalez… - Frontiers in …, 2014 - frontiersin.org
Viral infections remain a serious global health issue. Metagenomic approaches are
increasingly used in the detection of novel viral pathogens but also to generate complete …
increasingly used in the detection of novel viral pathogens but also to generate complete …
[HTML][HTML] VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Background Identifying viral sequences in mixed metagenomes containing both viral and
host contigs is a critical first step in analyzing the viral component of samples. Current tools …
host contigs is a critical first step in analyzing the viral component of samples. Current tools …
Identifying viruses from metagenomic data using deep learning
J Ren, K Song, C Deng, NA Ahlgren… - Quantitative …, 2020 - Wiley Online Library
Background The recent development of metagenomic sequencing makes it possible to
massively sequence microbial genomes including viral genomes without the need for …
massively sequence microbial genomes including viral genomes without the need for …
[HTML][HTML] VIROME: a standard operating procedure for analysis of viral metagenome sequences
KE Wommack, J Bhavsar, SW Polson, J Chen… - Standards in genomic …, 2012 - Springer
One consistent finding among studies using shotgun metagenomics to analyze whole viral
communities is that most viral sequences show no significant homology to known …
communities is that most viral sequences show no significant homology to known …
Challenges in the analysis of viral metagenomes
R Rose, B Constantinides, A Tapinos… - Virus …, 2016 - academic.oup.com
Genome sequencing technologies continue to develop with remarkable pace, yet analytical
approaches for reconstructing and classifying viral genomes from mixed samples remain …
approaches for reconstructing and classifying viral genomes from mixed samples remain …
[HTML][HTML] Recovering full-length viral genomes from metagenomes
SL Smits, R Bodewes, A Ruiz-González… - Frontiers in …, 2015 - frontiersin.org
Infectious disease metagenomics is driven by the question:“what is causing the disease?” in
contrast to classical metagenome studies which are guided by “what is out there?” In case of …
contrast to classical metagenome studies which are guided by “what is out there?” In case of …
ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data
Viruses are ubiquitous in humans and various environments and continually mutate
themselves. Identifying viruses in an environment without cultivation is challenging; …
themselves. Identifying viruses in an environment without cultivation is challenging; …
drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes
Background: Virus discovery using high-throughput next-generation sequencing has
become more commonplace. However, although analysis of deep next-generation …
become more commonplace. However, although analysis of deep next-generation …