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.
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.
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.
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.
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.
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.