Nirvana provides clinical-grade annotation of genomic variants (SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and SVs (including CNVs). It can be run as a stand-alone package, as an AWS Lambda function, or integrated into larger software tools that require variant annotation.

The input to Nirvana are VCFs and the output is a structured JSON representation of all annotation and sample information (as extracted from the VCF). Nirvana handles multiple alternate alleles and multiple samples with ease.

The software is being developed under a rigorous SDLC and testing process to ensure accuracy of the results and enable embedding in other software with regulatory needs. Nirvana uses a continuous integration pipeline where millions of variant annotations are monitored against baseline values daily.

Fun Fact

Nirvana is a backronym for NImble and Robust VAriant aNnotAtor

What does Nirvana annotate?

We use Sequence Ontology consequences to describe how each variant impacts a given transcript:

In addition, we also use external data sources to provide additional context for each variant:

Licensing

Code

Nirvana source code is provided under the GPLv3 license. Nirvana includes several third party packages provided under other open source licenses, please see Dependencies for additional details.

Data

The data used by Nirvana is publicly available, however some data sources have special restrictions on use by non-academic entities.

Nirvana Team

Active Team

The Nirvana team works on the core functionality, AWS annotation services, in addition to keeping the annotation data sources up-to-date.

Current members of the Nirvana team are listed in alphabetical order below.

Fahd Siddiqui

Joined our team back in December 2021 and brings even more cloud and ML experience to our team.

GitHub

Joseph Platzer

Test Lead. Joins Nirvana with a history of building sequencing tools and keeping the customer first.

GitHub

Rajat Shuvro Roy

Lead developer. Loves to speed up things and make services available to all interested users.

GitHub

Alumni

Nirvana would never be what it is today without the huge contributions from these folks who have moved on to bigger and greater things.

Elliott Margulies

Co-founder and former project sponsor.

GitHub

Haochen Li

Detail-oriented quick thinker that keeps cool even in the most stressful situations. Now working as a Senior Bioinformatics Data Scientist at GRAIL.

GitHub

Julien Lajugie

Julien is a legend around these parts. When he's not taking down opponents in Taekwondo or melting riffs in his rock band, he's demolishing bugs and making the world a better place.

GitHub

Michael Strömberg

Nirvana founder and former project lead.

GitHub

Ningxin Ouyang

Our newest addition to the team with a wealth of experience in transcript factor footprinting.

GitHub

Shuli Kang

Oncology bioinformatician from USC before joining our team at Illumina. Now working as a Senior Bioinformatics Scientist at Novartis Gene Therapies.

GitHub

Yu Jiang

Biostatistics genius from Duke University before joining our team at Illumina. Now working as a Research Engineer at Facebook AI Research.

GitHub