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Viral annotation software tools | Shotgun metagenomic sequencing data analysis

Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods (Mokili et al., 2012; Reyes et al., 2012). These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere.
Curator: Bonnie L. Hurwitz

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ViVan / Viral Variance Analysis
Allows users to study of throughput sequencing (HTS) data with the aim of standardizing and facilitating the analysis. ViVan is a pipeline available as both a web application and a standalone software that consists of HTS data analysis tools coupled to Python scripts. The analysis is composed of six main steps: (i) quality control, (ii) alignment and Pileup, (iii) variant frequency collection and filtering, (iv) variant annotation, (v) per-sample metrics and supplements and (vi) group comparison.
EzMap
Performs metagenomic analysis of the human virome. EzMap combines a number of tools to clean, filter, and subtract whole-genome sequencing (WGS) reads by mapping to a reference human assembly. It is automated to run on both workstations and computing clusters for all steps. The tool automates an otherwise tedious and time-consuming protocol and aims to facilitate rapid and reproducible insights from cfDNA. It allows the relative abundance of all known viruses in a sample to be determined based solely on DNA sequence.
VIP / Virus Identification Pipeline
A one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related reads, (ii) extensive classification of reads on the basis of nucleotide and remote amino acid homology, (iii) multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight. We validated the feasibility and veracity of this pipeline with sequencing results of various types of clinical samples and public datasets. VIP has also contributed to timely virus diagnosis (~10 min) in acutely ill patients, demonstrating its potential in the performance of unbiased NGS-based clinical studies with demand of short turnaround time.
Vipie
Permits to make parallel characterization of viral population from multiple Next Generation Sequencing (NGS) samples. Vipie is able to perform de-novo assembly, taxonomic classification of viruses as well as sample analyses. It can identify all agents present in the dataset and in the final step it attempts remapping of the original reads from every sample to this whole reference set. This tool identifies all agents present in the dataset and in the final step it attempts remapping of the original reads from every sample to this whole reference set.
ViromeScan
An innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. ViromeScan uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites. By enabling an efficient detection of the viral counterpart from shotgun sequencing, ViromeScan extensively integrates the analysis of the microorganisms that inhabit the human body. Furthermore, ViromeScan can be applied to any environment as a tool for taxonomic profiling of the virome with resolution up to species level. An interesting and flexible aspect for users is that the pipeline of analysis can also be used with a customized database containing viral genomes of interest.
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