Java framework for reading, writing, analyzing and manipulating sequence and assembly data. Jillion supports most common data file formats used in bioinformatics and supports both Sanger and Next-gen data.

The Java Informatics Large LIbrary fOr geNomics (Jillion) is an open source genomics software framework written in Java 8 to support bioinformatics. This library was created by Dan Katzel at the J. Craig Venter Institute (JCVI) and used by several projects including The Influenza Genome Project, Leptospira and the Human Microbiome Project and used in over 20,000 viral whole and draft genome submissions to Genbank.

The framework consists of objects and utilities allowing to parse and write files in the most popular sequencing file formats and manipulating efficiently a large number of sequencing reads, creating and manipulating sequence alignments, etc.


This work has been funded in whole or part with federal funds from the Genomic Sequencing Centers for Infectious Diseases (GSCID) and the Genomic Centers for Infectious Diseases (GCID), part of National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH).

Principal Investigator

Key Staff

  • Lihui Hu, PhD


Related Research


Dan Katzel
Rancho BioSciences