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Download OmicsBox

Download OmicsBox 3.1

Download here the latest version of OmicsBox for free (on the right). The download contains an executable installer which will install OmicsBox on your computer. Choose between Windows, Mac or Linux based versions.

Get the Installer from here:

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How do I get an activation key?

Just click here and register with your name and email and we will send you your key immediately. Registration takes less than 1 minute.

System Requirements

  • We recommend at least 4GB of RAM. 
  • A stable internet connection is required to use many of the application features. 
  • OmicsBox is available for Mac (10.14+), Windows (7+) and Linux systems (Ubuntu 18.04+, Debian 8+, RedHat Enterprise Linux 7, CentOS 7+). The Linux systems require the library version GTK 3.22+. 
  • OmicsBox supports automatic updates (write permissions required).

Please find more details in the User Manual under System Requirements.

Release History and Versions

Functional Analysis
  • Removed MobiDB-Lite from InterProScan due to the lack of GO information
Genetic Variation
  • Fixed Issue when Saving MAGMA Objects
Transcriptomics
  • Fixed GTF/GFF Input for STAR
  • Fixed Issue for Cell-Barcoded and Full-Length Modality in STARsolo
  • Fixed Single-cell Dimensionality Check for Count Matrix Import
  • Improved STARsolo Chart for Genes Distributions in Percentages
Metagenomics
  • Fixed Pairing Factor Issue of the Differential Taxonomic Abundance Analysis.
General
  • More Specific Task Error Messages
Functional Analysis
  • New Bubble Plot for GSEA
  • Updated GO-Slim Links
  • Fixed GO Annotation Taxa Filtering
Transcriptomics
  • Added Single-Cell Count Matrix Dimension Check for MTX Format
  • Improved Single-Cell Quantification Summary Report
  • Fixed Bug in the STARsolo Wizard
  • Changed maSigPro to apply a Negative Binomial Distribution
  • Fixed Numeric x-Axis for maSigPro Expression Profiles
Metagenomics
  • Updated Pfam2GO Links
Genetic Variation
  • Fixed Variant Annotation for Poliploides
General
  • Improved File-Upload Resilience for CloudFiles
  • Minor CloudFiles Improvements

Transcriptomics

  • New Single Cell RNA-Seq Quantification Feature with StarSolo
  • Improved Single Cell RNA-Seq Clustering with Interactive UMAPs
  • Improved Single Cell RNA-Seq Trajectory Visualizations: Gene Trends and Expression UMAPS
  • New Long-Read Aligner: Minimap2

Genetic Variation

  • New Functional Analysis of GWAS Results with MAGMA
  • New Variant Calling Option for Mixed-ploidy in Freebayes
  • New feature to extract variant information from Variant Annotation using Manhattan Plots

General

  • Improved Barcode Demultiplexing Supporting Paired-Ends
  • Improved Job Progress and Status Messages
  • Improved Proxy Configuration and Authentication

Metagenomics

  • Custom Kraken DB Option for Taxonomic Classifications

Functional Analysis

  • Custom Diamond Blast DB Option

Genetic Variation Module

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

Transcriptomics

  • Isoform Definition and Correction with Flair

Functional Analysis 

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

Genome Analysis

  • Genome Assembly Comparision and Qualitiy Assessment with QUAST

General Tools

  • Barcode Demultiplexing with Cutadapt

General Improvements

  • Redesigned Functional Enrichment Analysis Options throughout OmicsBox
  • Improved Message Handling for Cloud Jobs
  • Option to share Cloud Files

General Tools

Transcriptomics Module

General Improvements

  • Restructuring of Menus and Side Panel Options for improved usability
  • Introduction of CloudStorage
  • Improved Workflows

Transcriptomics Module

  • New Heatmap and PCA 2D/3D Plots
  • New Single Cell Clustering Option
  • Coding Potential Assesment now part of the Transcriptomics Module

Genome Analysis Module

  • MLST feature as part the Genome Analysis Module
  • Genome Browser now part of the Genome Analysis Module

Functional Analysis

  • Plant Reactome Database for Combined Pathway Analysis
  • New Pathway Analysis Charts
  • Subcellular Localization Prediction with Psortb

Functional Analysis

Transcriptomics Module

  • De-novo Isoform Discovery for PacBio Long Reads (Iso-Seq)
  • Updates for Trinity (2.12.0), BUSCO (5.1.2) and STAR (2.7.8a)

Metagenomics Module

  • rRNA Removal with SortMeRNA
  • Contaminant Removal with Bowtie2
  • Kraken and Pfam (v.34.0) Database Updates

Genome Analysis Module

  • New DNA-Seq Alignment with Bowtie 2
  • Improved Eukaryotic Gene Finding with Augustus
  • Updates for ABySS (2.3.0), SPAdes (3.15.2), Flye (2.8.2), Augustus (3.4.0) and RepeatMasker

General Tools and Improvements

Metagenomics Module

  • Taxonomic Classification: Kraken2 database update and new parameters
  • Taxonomic Classification: New option to add, remove and rename samples
  • Taxonomic Classification: Improvements to bar chart

Transcriptomics Module

  • RNA-Seq de novo Assembly: Trinity update (v2.10.0), improved performance and new parameters
  • GSEA for Pairwise DEA: Ranking is now based on p-values instead of the FDR
  • RNA-Seq Alignment: STAR update (v.2.7.5a) and new reference fasta file format (.gz)
  • RNA-Seq Alignment: New parameter to include Read Group (@RG) header and tags in BAM output
  • Create Count Table Transcript-Level: RSEM update (v.1.3.3)

Genome Analysis Module

  • DNA-Seq Polishing: Improved performance due to parallelized analysis
  • DNA-Seq Alignment: New reference fasta file format (.gz)
  • DNA-Seq Alignment: New parameter to include Read Group (@RG) header and tags in BAM output
  • DNA-Seq Assembly (Flye): Flye Update (v.2.8) and support of PacBio HiFi data
  • MLST: Database update and wizard improvements

Functional Analysis

  • BLAST: New feature “Custom DB Cloud Blast” to run blast against own fasta file

General

  • Genome Browser: New reference fasta file format (.gz)
  • File Manager: Fixed issue with “Merge Objects”
  • Make Blast DB Fix: Internal parameter for win64: BLASTDB_LMDB_MAP_SIZE
  • Fisher’s Exact Test: Fixed dialog link and GO selection
  • Taxonomic Classification: Improve memory management and improved report formatting
  • BWA: Improved name for BAM file output
  • Genome Browser: Fixed issue with region selection while scrolling
  • FASTQ Preprocessing: Fixed workflow permissions
Metagenomics Module
  • Differential Abundance Analysis of Functions and Pathways (EggNOG and Pfam)
  • Taxonomic Classification with Kraken: Update to v.2
Transcriptomics Module
  • RNA-Seq Alignment with BWA
  • Sequence Clustering with CD-HIT
  • Trinity accepts FASTA read files as input
  • Completeness Assessment with BUSCO: Update to v.4 and OrthoDB v.10
Genome Analysis Module
  • Long-Read De-Novo Assembly and Polishing with Flye and Pilon
  • DNA-Seq Alignment with BWA
  • DNA-Seq De-Novo Assembly SPAdes: Update to v.3.14
General Tools
  • Filter Fasta by Length
  • Convert FastQ to Fasta
  • Improved Venn Diagram

Metagenomics Module

  • New Taxonomic Classification Statistics: Chao1 OTU Diversity, Rarefaction Curves and PCoA Plot
  • OTU Differential Abundance Testing with edgeR

Transcriptomics Module

  • Completeness Assessment with BUSCO
  • Predict Coding Regions with TransDecoder
  • Improved RNA-Seq Alignment Input: GFF is automatically converted to GTF
  • New RNA-Seq Alignment Options: 2-Pass mode, Export Spliced Junctions, Export Unmapped Reads
  • New RNA-Seq De Novo Assembly Option: SuperTranscripts
  • Export Normalised Counts of TimeCourse Results
  • Export Normalised Counts of Pairwise Differential Expression Without Replicates Results

Genome Analysis Module

  • De-Novo Assembly with SPAdes
  • Repeat Masking Database Update DFAM v.3
  • Repeat Masking Compatibility with RepBase 2017 and 2018
  • Improved Wizard for Sample Selection

General Tools

  • Barcode Splitter Tool
  • New Example Workflows

General

  • Minor visual improvements

Transcriptomics Module

  • Create Count Table (Gene-level): Memory usage improvements
  • Differential Expression Analysis: Heatmap minor improvements
  • RNA-Seq Alignment: Fix bug with fastq files

Metagenomics Module

  • Taxonomy Classification: Fix report
  • GO Graphs: new option to export the visible region
  • Generic Export: new options for start/end query and HSP positions in BlastHits
  • Table Viewer: fix scroll issue causing hidden bottom rows
  • License: fix the restart loop when using limited mode after key expired
  • Blast Results: fix tooltip
  • Genome Browser: fix a specific region position issue
  • CloudBlast: skip sequences longer than 100k symbols
  • Create Count Table: fix download BAM files issue when “Generate Alignment Files” is selected

General

  • Fix minor issue regarding citations in wizards

Metagenomics Module

  • Fix bug in metagenomics workflows causing tasks to fail

Functional Analysis Module

  • Make Blast DB: Taxonomy Map file can be plain text

General

  • Allow opening OmicsBox in viewer mode when offline
  • Fix: Welcome window sometimes not showing content on MacOS
  • Fix: Update previously installed Apps on platform update
  • Improvement: Check fastq.gz files for corruption

Transcriptomics Module

  • RNA-Seq De Novo Assembly: two additional parameters
  • RNA-Seq Alignments: fix output BAM files name
  • Differential Expression: improve files parser to skip headers

Genome Analysis Module

  • Repeat Masking: unknown species are rejected by the validator

Metagenomics Module

  • Fixed problem with white spaces in filenames
  • Updated Kraken database to 2019.06
  • Improves Krona viewer styling

Functional Analysis Module

  • InterProScan: remove deprecated ProDom search option
  • Rfam: fix ‘end’ column not showing data

General

  • Improved citations in wizards and reports
  • Example Data Import option

Transcriptomics Module

  • RNA-Seq Alignment against reference genome (STAR)

Genome Analysis Module

  • DNA-Seq De Novo Assembly (ABySS 2.0)
  • Repeat Masking (RepeatMasker)

Metagenomics Module

  • Taxonomic Classification (Kraken)
  • Metagenomic Assembly (MEGAHIT and meta-SPAdes)
  • Metagenomic Gene Prediction (FragGeneScan and Prodigal)

Functional Analysis Module

  • New CloudBlast taxonomy filtering
  • Improved CloudIPS speed and resource usage
  • New EC class (7)

Jan. 2019

  • Blast2GO is now OmicsBox
  • Search box for menu actions
  • New menu structured by modules
  • Bug fixes and improvements
  • New Module: Metagenomics

OMICSBOX MODULES

OmicsBox is a bioinformatics software solution which allows to get from reads to insights with ease. Use OmicsBox for the NGS data analysis of genomes, transcriptomics and metagenomes.

OmicsBox is structured in Modules. Depending on your needs you can combine different modules required for your data analysis.

  • 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
  • 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

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.

Over 500 Institutions around the world trust OmicsBox