Dataset Information

VirAmp: a galaxy-based viral genome assembly pipeline.

ABSTRACT: BACKGROUND:Advances in next generation sequencing make it possible to obtain high-coverage sequence data for large numbers of viral strains in a short time. However, since most bioinformatics tools are developed for command line use, the selection and accessibility of computational tools for genome assembly and variation analysis limits the ability of individual labs to perform further bioinformatics analysis. FINDINGS:We have developed a multi-step viral genome assembly pipeline named VirAmp, which combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. Our pipeline allows users to assemble, analyze, and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices into a single, easy to use interface. We tested our pipeline with three different datasets from human herpes simplex virus (HSV). CONCLUSIONS:VirAmp provides a user-friendly interface and a complete pipeline for viral genome analysis. We make our software available via an Amazon Elastic Cloud disk image that can be easily launched by anyone with an Amazon web service account. A fully functional demonstration instance of our system can be found at http://viramp.com/. We also maintain detailed documentation on each tool and methodology at http://docs.viramp.com.

SUBMITTER: Wan Y

PROVIDER: S-EPMC4410580 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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VirAmp: a galaxy-based viral genome assembly pipeline.

Wan Yinan Y Renner Daniel W DW Albert Istvan I Szpara Moriah L ML

GigaScience 20150428

<h4>Background</h4>Advances in next generation sequencing make it possible to obtain high-coverage sequence data for large numbers of viral strains in a short time. However, since most bioinformatics tools are developed for command line use, the selection and accessibility of computational tools for genome assembly and variation analysis limits the ability of individual labs to perform further bioinformatics analysis.<h4>Findings</h4>We have developed a multi-step viral genome assembly pipeline ...[more]

PMID: 25918639

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Project description:BackgroundGene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological, and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL, and HomoloGene, to identify gene families and visualize syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries among multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences, provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.FindingsA certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we converted this pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow.ConclusionsGeneSeqToFamily represents the Ensembl GeneTrees pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy's user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualize the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

Dataset Information

VirAmp: a galaxy-based viral genome assembly pipeline.

Publications

VirAmp: a galaxy-based viral genome assembly pipeline.

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