OmicsBox 3.0 Release: New Module and Features

OmicsBox 3.0 Release: New Module and Features

Once again we are pleased to announce the latest update of OmicsBox 3.0.

The whole BioBam team has worked to bring the new version of the BioBam bioinformatics solution to life.

We proudly present the Genetic Variation Module as the highlight of OmicsBox 3.0. This module enables variant calling, filtering, and annotation, as well as the association of genetic variations with a specific trait or disease via genome-wide association studies.


Genetic Variation: all you need to know about our new module

The module offers two different analysis strategies for variant calling and filtering. Many options are available to adjust the analysis to specific methodologies like e.g GBS vs WGS or different requirements like the level of ploidy, genome coverage, or the presence of repetitive regions. This combination of tools has been shown to outperform alternative pipelines in several recent review studies (e.g. Nature Sci. Rep. 12, 11331 (2022)). The module also allows the execution of guided genome-wide association studies (GWAS) to identify genetic variations associated with a particular trait. More details about the novel Genetic Variation module can be found here: Genetic Variation Module.


“To be able to analyze genetic variation with OmicsBox is highly requested by our user community and something that has been on our roadmap for a long time. It makes me especially happy to be now able to announce a robust and highly efficient combination of state-of-the-art tools for performing genetic variation analysis within OmicsBox. I am eagerly looking forward to seeing how this module will assist our users in advancing their research and making faster discoveries.”

Dr. Stefan Götz, CEO of BioBam Bioinformatics S.L.


Please find below a list of feature highlights and improvements.

OmicsBox 3.0 new features:

Genetic Variation Module

  • Fast Variant Calling with BCFtools and FreeBayes
  • Variant Filtering
  • Variant Annotation with Variant Effect Predictor (VEP)
  • Guided Genome-Wide Association Study

Genome Analysis

  •  Genome Assemblies Comparison and Quality Assesment with QUAST


  • Long Read based Isoform Definition and Correction with FLAIR

Functional Analysis

  • Faster Functional Annotation with Diamond Blast
  • KEGG Pathways Analysis available for commercial customers

General Tools

  • Barcode Demultiplexing with Cutadapt

About OmicsBox:

OmicsBox is a leading bioinformatics solution that offers end-to-end NGS data analysis of genomes, transcriptomes, and metagenomes. The application is used by top private and public research institutions worldwide and allows researchers to easily process large and complex data sets, and streamline their analysis process. It is designed to be user-friendly, efficient, and with a powerful set of tools to extract biological insights from omics data.

The software is structured in different modules, each with a specific set of tools and functions designed to perform different types of analysis, such as de-novo genome assemblies, genetic variation analysis, differential expression analysis, and taxonomic classifications of microbiome data, including the functional interpretation and rich visualizations of results. The functional analysis module, which includes the popular Blast2GO annotation methodology makes OmicsBox particularly suited for non-model organism research. Over 15k scientific research citations demonstrate this. OmicsBox works out of the box on any standard PC or laptop with Windows, Linux, or Mac.

How to update?

  • OmicsBox will update automatically. If you are working with OmicsBox 2.0 or higher you don’t have to do anything to update to the latest version.
  • If you are still using Blast2GO PRO we highly recommend upgrading to OmicsBox. You can download the latest version here


Feedback, questions, and feature requests are most welcome. Please write to support@biobam.com or log in to your BioBam Account.


omicsbox 3.0 release

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