The name Elvira stands for Executive for Large-scale VIRal Assembly. Elvira is a collection of tools and scripts used at JCVI for sequence and metadata tracking, sequence assembly, coverage and other analysis, and generation of reports.

The majority of the code is written in Java (ElviraJava), with several Perl and PHP scripts and libraries.

Elvira was developed at TIGR (now JCVI) where it contributed to the sequencing and publication of thousands of viral genomes. This software is designed to interact mostly with CLC Bio command line tools and with proprietary VGD schema databases.

ElviraJava is written in Java 8 and is based upon the Jillion framework.


This software was developed at The Institute for Genomic Research (TIGR) and at JCVI with financial assistance from the Microbial Sequencing Centers (MSC), Genome Sequencing Centers for Infectious Diseases (GSCID), and Genomic Centers for Infectious Diseases (GCID), part of the National Institute of Allergy and Infectious Disease (NIAID) at the National Institutes of Health (NIH).

Principal Investigator

Key Staff

  • Lihui Hu, PhD


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