Viral annotation software tools | Shotgun metagenomic sequencing data analysis
Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere.
Determines and ranks low coverage and highly divergent viruses into metagenomic information. VirMAP is a program employing multiple methods including a combination of de-novo and mapping assembly strategies as well as a taxonomic classification algorithm. It is able to perform its analysis without considering coverage depth and includes features to adjust both sensitivity and specificity tradeoff.
Allows investigation of raw or assembled viral metagenomes. METAVIR offers users a solution to exploit their metagenomics data. It can be applied to viromes composed of raw reads, mostly generated using pyrosequencing technology and to viromes assembled into contigs, a strategy possible with datasets sequenced with either pyrosequencing or Illumina technology. This tool is useful to study the similarities between virome reads and a viral genome of interest.
Identifies prokaryotic viral sequences from metagenomic data. VirFinder is a k-mer based program using machine learning methods to identify sequence signatures. It distinguishes viral sequences from host sequences, and as a result, constructs a scoring system to predict viral sequences based on sequence signatures. It was developed to find and analyze viral sequences in human gut metagenomic data from healthy and liver cirrhosis patients.
Performs computation of maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods. CatchAll is a set of two programs for analyzing data derived from experiments or observations of species abundances or multiple recapture counts comprising: (1) the main analysis program and (2) an interactive graphics module written in Excel 2007.
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.
Provides a method for specific detection and quantification of human papillomavirus (HPV) from metagenomic data. HPViewer is an HPV discovery program that reduces false determination of HPV DNA by masking simple repeats commonly shared among the human genome, prokaryotes, and homologous sequences shared by different HPV types. The homology-mask mode of HPViewer can reduce misclassification of reads.
Finds metagenomic next generation sequencing (NGS) data. VIP classifies reads against reference databases (DB) collected by Virus Pathogen Resource (ViPR) and Influenza Research Database (IRD) nucleotide DB. It includes a variety of clinical infections, detected pathogens, sample types, and depths of coverage. This tool makes multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight.
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.
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.
Identifies and quantifies the abundance of viruses in metagenomics data. FastViromeExplorer is a stand-alone pipeline that uses kallisto to map short reads to a reference virus database and then filters the alignment results and reports virus types and abundances along with taxonomic annotation. The software allows researchers that have limited computing power to process large metagenomic data within reasonable time.
Assists users with annotation and GenBank deposition of viral genomes. VAPiD supports annotation of unsegmented viral genomes. This program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated.
Assists users to perform annotation of prokaryotic and eukaryotic viral sequences from (meta)genomic studies. VIGA detects open reading frames from a FASTA or multi-FASTA formatted file. Moreover, this tool includes features for detection of: (1) the topology of viral contigs; (2) the presence of rRNA, tRNA and tmRNA sequences; (3) potential CRISPR repeats and (4) tandem or inverted repeat sequences.
Identifies viruses form metagenomics data. ViruSpy consists of three steps: (1) identification of viral reads in the samples using Magic-BLAST, (2) assembly and annotation of extracted raw reads into contigs via MEGAHIT, Glimmer (for genes) and RPS-tBLASTn (for conserved domains), and (3) determination of whether the viral genomes are non-native to a host genome, using the Building Up Domains (BUD) algorithm.
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.