OmicsBox 3.2 Release

OmicsBox 3.2 Release

We are happy to announce the latest update of OmicsBox 3.2.

“I am particularly happy to announce that with our latest release, our team managed to create a straightforward yet sophisticated solution for the challenging domain of Single Cell Transcriptomics. This marks a significant enhancement to the suite of complex analysis scenarios OmicsBox simplifies, including also Long-Read Transcriptomics, a field still in the process of defining its analysis protocols and with OmicsBox already offering a broad array of options.”

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

Key highlights of this release include enhanced visualization and cell-type annotation features for Single Cell Transcriptomics data analysis. Single Cell data analysis, inherently exploratory, benefits greatly from the new annotation and visualization options, enabling the integration of various tools and datasets to unravel tissue complexities using approaches like trajectory analysis and differential expression analysis of cell groups.

The Genetic Variation Module has also seen several significant updates, including the capability to perform population structure analysis and additional tools for VCF data manipulation, filtering, phasing, and imputation. These enhancements culminate in a comprehensive toolkit for end-to-end genetic variation analysis.

Please find below a list of feature highlights and improvements:

OmicsBox 3.2 new features and improvements :

Single Cell Transcriptomics

  • New: Cell Type Identification with SingleR
  • Update: Interactive Single-Cell Visualization and Annotation Tool
  • Update: Seurat v.5
  • Update: Improved Trajectory Analysis with Monocle
  • New: Autocorrelation Analysis via Monocle3

Long Read Transcriptomics


  • Update: Busco Database – Update: EdgeR v.4
  • Improved Gene-Level Quantification with HTSeq Count (now cloud based)

Genetic Variation

  • New: Merge and Extract VCF Files
  • New: Population Structure Analysis with ADMIXTURE
  • New: Imputation and Phasing with Beagle
  • New: Filtering for GBS data via dDocent Pipeline

Genome Analysis

  • Update: Evidence-based eukaryotic gene predictions with Augustus

Functional Analysis

  • New: Find Pathways via Annotations


  • Improved Trimmomatic Wizard (now cloud based)
  • Improved Application Messages
  • OmicsBox now available for macOS ARM architecture

About OmicsBox:

BioBam’s bioinformatics solution offers a user-friendly data analysis platform that allows getting from next-generation sequencing reads to biological insights with ease.

OmicsBox offers “out-of-the-box” data analysis and functional interpretation of genome, transcriptome, and metagenome datasets for industry, academic, and governmental research biologists. OmicsBox is used by top private and public research institutions worldwide.

OmicsBox is structured in the following modules and can be configured as required: Genome Analysis, Transcriptomics, Functional Analysis, and Metagenomics. The Functional Analysis module includes the Blast2GO functional annotation methodology and makes Omicsbox especially popular in non-model organism research with over 10.000 scientific citations.

OmicsBox relies on cloud computation for all resource-consuming tasks like for example genome assemblies or any other CPU or memory-consuming algorithms. All these computationally challenging bioinformatics pipelines can be run transparently with OmicsBox from any standard PC or laptop on Windows, Linux, or Mac. OmicsBox is based on a subscription model with very flexible licensing options. Please contact us for more information.

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.

About the Author Paula Cubilles Paula is a versatile professional with a background in visual arts, design, and branding. With her expertise in communication and marketing, Paula brings a creative and strategic approach to BioBam's brand.

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