OmicsBox Test

Bioinformatics made easy

  • Quality Control And Assessment
  • De-Novo Assembly
  • Repeat Masking
  • Gene Finding
  • Coding Potential
  • Fast Variant Calling
  • Model & Non-Model Variant Annotation
  • Variant Filtering
  • Guided Genome-Wide Association Studies
  • Supports GBS and WGS data
  • Quality Control
  • Quantify Expression
  • De-Novo Assembly
  • RNA-Seq Alignment
  • Differential Expression Analysis
  • High-Throughput Blast and InterProScan
  • Gene Ontology Mapping
  • Blast2GO Annotation
  • Enrichment Analysis
  • Functional Interpretation
  • Quality Control And Assessment
  • Taxonomic Classification
  • Metagenomic Assembly
  • Gene Prediction
  • Functional Annotation

The All-In-One Bioinformatics Software

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.



Ready to use

OmicsBox Modules

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. This is demonstrated by over 15k scientific research citations. OmicsBox works out of the box on any standard PC or laptop with Windows, Linux, or Mac.

Genome Analysis Module

The Genome Analysis module allows to characterize and analyze newly sequenced genomes, from raw reads to gene structures in an efficient and user-friendly way. Use FastQC and Trimmomatic to perform the quality control of your data, filter reads, and remove low-quality bases. The assembly feature allows the reconstruction of whole genome sequences without a reference genome and specific hardware requirements. 

genome analysis module
Genetic Variation

Genetic Variation Module

The Genetic Variation Module allows for performing variant calling, filtering, and annotation, as well as associating genetic variations with a particular trait or disease via genome-wide association studies.

The module offers two different analysis strategies for variant calling and filtering based on the popular tools, BCFtools and FreeBayes. Many options are available to adjust the analysis to specific methodologies (e.g GBS vs WGS) or requirements (level of ploidy, genome coverage, presence of repetitive regions, etc.). 

Transcriptomics Module

The Transcriptomics module allows for the processing of RNA-Seq data from raw reads down to the functional analysis in a flexible and intuitive way. Once quality control has been applied using FastQC and Trimmomatic, RNA-seq data can be aligned to a reference genome using STAR or BWA, or assembled without a reference genome using Trinity to obtain a de-novo transcriptome. Additional tools for predicting coding regions and assessing coding potentials aid in refining the datasets. The module also allows quantification of expression at the gene or transcript level – with or without a reference genome, using HTSeq or RSEM. Different statistical charts provide information about the assembly and quantification processes, as well as a quality assessment of the results. 

Transcriptomics Module

Functional Analysis Module

The Functional Analysis module allows adding biological context to the different data analysis approaches.

An initial step is the functional annotation of any given dataset. The popular Blast2GO methodology allows flexibility to assign the most reliable functional labels to novel sequence datasets. The annotation process takes into account source annotation quality and Gene Ontology hierarchies. Cloud-based Blast and InterPro allow for fast sequence alignment and domain searches against the reference datasets of your choice. Potential homologs and domains are linked to functional annotation from up-to-date and well-curated databases like UniProt and the Gene Ontology Consortia.

Metagenomics Module

The Metagenomics Module enables the execution of different types of microbiome data analysis, including the assembly, annotation, and classification of metagenomic data. It allows to combine and integrate all necessary steps for a complete microbiome data analysis in a flexible and intuitive way and offers custom pipelines for individual analysis strategies.
The module offers Kraken to identify bacteria, archaea, fungi, protozoa, and viruses down to strain levels. Rich visualizations help to gain insights more easily. With the tools MetaSPAdes and MEGAHIT it is possible to assemble large datasets easily and fast in the cloud. 

OmicsBox Base Platform

Manage Projects and Files, Access to Cloud Computing, Design, Run and Save Workflows, Visualize Data, Genome Browser, Filter and Sort Large Tables, General Bioinformatics Tools, and More.

  • Workflows
  • Genome Browser
  • FastQC Quality Control Tools
  • Generic Charts (Bar, Pie, etc.) and Venn Diagrams
  • Access to File Manager, Support Mail, App Manager, Cloud Usage
  • Load, View and Export all supported file types (.box, .b2g, .fasta, . fastq, .gff, .vcf., .bam, etc.)

Get Started with a Free Trial

Get familiar with all new Modules and Features.
OmicsBox works out of the box on any standard PC or laptop with Windows, Linux and Mac. 

Over 500 Institutions around the world trust OmicsBox

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