Viral integration site detection software tools | Whole-genome sequencing data analysis
Some viruses have the ability to integrate the host genome, leading in some cases to epigenetic and genetic alterations, and oncogenesis. Whole-genome sequencing is a powerful technology to identify viral sequences integrated in host genome. Virus detection software tools use algorithms and read alignment to identify viral sequences from whole-genome sequencing data.
Implements an extensive array of methods for detecting and visualizing recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 can analyze up to 2500 sequences that can reach 10Mb. It is also applicable to the analysis of bacterial full-genome sequence datasets. It uses either fully automated mode from the command line interface or with a graphical user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.
Performs all necessary computational analysis steps; including reference genome library extraction and indexing, read quality control and alignment, strain identification, and summarization and annotation of results. PathoScope 2.0 is a complete bioinformatics framework for rapidly and accurately quantifying the proportions of reads from individual microbial strains present in metagenomic sequencing data from environmental or clinical samples.
Detects and annotates genome-wide viral fusions and breakpoints. VFS proposes a method that exploits high-throughput sequencing (HTS) for performing analysis at single-base resolution. This application can also recreate fusion transcripts leaning on a combination of clipped sequence and discordant read pair (RP) information. Its analysis can be applied to both DNA and RNA-seq information.
Describes intra-host viruses through next generation sequencing (NGS) data. VirusFinder retrieves virus infection, co-infection with multiple viruses, mutations in the virus genomes, in addition to virus integration sites in host genomes. It reports novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. This tool deals with both paired-end and single-end data.
Conducts de novo reconstruction of novel viruses and retrieves already identified viral species from sequencing datasets. Metavisitor is included into the galaxy platform and permits users to add investigation steps or to replace/modify existing ones. It assists researchers in field surveillance of insect vectors and emerging viral species during epidemics, in viral metagenomic studies or in experimental research or diagnosis for human patients suffering from viral infections or coinfections.
Discovers the presence of pathogens from a custom reference in high-throughput sequencing datasets. RIND is designed for mate-paired high-throughput sequencing data with reads at least 36 bp and up to 500 bp. It is useful for sequencing data from any species. This tool enables the discovery of sequencing reads from intact or mutated non-human genomes in a dataset and constructs contigs with these non-human sequences.
Maps the reads to reference genomes. VirFind is a method specifically developed for virus detection and discovery able to: (i) map and filter out host reads, (ii) deliver files of virus reads with taxonomic information and corresponding Blastn and Blastx reports, and (iii) perform conserved domain search for reads of unknown origin. The pipeline was used to process more than 30 samples resulting in the detection of all viruses known to infect the processed samples, the extension of the genomic sequences of others, and the discovery of several novel viruses.