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CoVaCS: Consensus Variant Calling System

The Consensus Variant Calling System

CoVaCS is an automated, highly accurate workflow for genotyping, variant calling and annotation for Next Generation Sequencing data. By integrating state of the art tools and algorithms in a swift and effective manner and providing a extensive collection of reference genomes, CoVaCS offer the possibilty to perform elaborate and comprehensive genotyping of NGS data even to users with little or no bioinformatic background.

CoVaCS is currently hosted at CINECA and benefits all the advantages of HPC computing.
In its current form CoVaCS offers pre-configured workflows for the analyses of WGS, WES and targeted resequencing data.
All the workflows are very simple to use and require little configuration by the users:

WGS workflow: to be used if your data is complete shotgun sequencing of any of the reference genomes in CoVaCS, all you need to do is tell CoVaCS which reference genome is to be used.

WES workflow: if you performed exome sequencing on any of man,mouse or cow, CoVaCS is capable to handle all the major commercial exome kits (Illumina, Agilent or Nimblegen) for you, all you have to do is select the right kit (and reference genome!) from the dropdown menu.

Targeted resequencing workflow: this workflow is intended for targeted resequencing experiments, but it comes handy also in the case where you can't find your exome kit enlisted among the kits included in CoVaCS. To inform the system of the target regions, you will have to supply CoVaCS the coordinates in the format of a bed file. Please be sure to that your file matches the same version of the genome assembly you are intend to use before starting any analyses.

CoVaCS is designed to offer a simple stremalined, GUI driven workflow for the analysis of NGS resequencing data, as such the user is given little or no means to modify the behaviour of our workflows. If you are an advanced user and feel the need of a more elaborate and customizable pipeline for genotyping, you can use the command line based version of CoVaCS.

BMC Genomics 201819:120. 5 February 2018. doi: 10.1186/s12864-018-4508-1
CoVaCS: a consensus variant calling system.
Chiara M, Gioiosa S, Chillemi G, D'Antonio M, Flati T, Picardi E, Zambelli F, Horner DS, Pesole G, Castrignanò T.

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