OmicsBox

OmicsBox, developed by BioBam, is an all-in-one bioinformatics software platform designed to provide end-to-end next-generation sequencing (NGS) data analysis across genomics, transcriptomics, and metagenomics. It is used by over 500 top private and public research institutions worldwide and is particularly well-suited for researchers working with non-model organisms, thanks to its integration of the widely cited Blast2GO annotation methodology. With more than 15,000 scientific research citations, OmicsBox is trusted by molecular biologists, ecotoxicologists, genome analysts, and computational biologists seeking a powerful yet accessible solution for complex omics data analysis.

The platform is structured into specialised modules, each containing a dedicated set of tools for a specific type of analysis. OmicsBox is designed to be user-friendly and ready to use out of the box on any standard PC or laptop running Windows, Linux, or Mac, removing the need to install individual bioinformatics tools separately. A base platform underpins all modules, providing project and file management, cloud computing access, workflow design and execution, a genome browser, data visualisation, and support for all major file types including .fasta, .fastq, .gff, .vcf, and .bam.

Functional Analysis Module

• Implements the Blast2GO methodology to assign reliable functional labels to novel sequences using cloud-based Blast, InterPro, and EggNog searches for alignment, domain, and orthology information
• Supports high-throughput Blast and InterProScan for large-scale sequence annotation
• Gene Ontology (GO) mapping provides biological context for annotated sequences
• Enrichment analysis using Fisher's Exact Test and GSEA identifies over- and underrepresented biological functions
• Combined Pathway Analysis identifies Reactome and KEGG pathways for any sequence set, enabling pathway enrichment calculation and rich visualisations

Transcriptomics Module

• Processes RNA-Seq data from raw reads through to functional analysis in a flexible and intuitive workflow
• Quality control followed by alignment to a reference genome using STAR or BWA, or de-novo transcriptome assembly using Trinity
• Expression quantification using HTSeq or RSEM, with coding region prediction also available
• Differential expression analysis using statistical packages including NOISeq, edgeR, and maSigPro
• Long-read transcriptomics analysis is supported
• Single-Cell RNA-Seq tools identify cell groups and lineage trajectories
• Integrated enrichment analysis to identify over- and underrepresented biological functions

Genetic Variation Module

• Supports fast variant calling and filtering using BCFtools and FreeBayes
• Compatible with both Genotyping-by-Sequencing (GBS) and Whole Genome Sequencing (WGS) data
• VCF file annotation via the Variant Effect Predictor from Ensembl, supporting both model and non-model organism annotation
• Guided Genome-Wide Association Studies (GWAS) to identify genetic variations associated with particular traits or diseases
• Tool combination has been shown to outperform alternatives in recent review studies

Metagenomics Module

• Taxonomic classification using Kraken, identifying microorganisms down to the strain level
• Metagenomic assembly of large datasets using MetaSPAdes and MEGAHIT in the cloud
• Gene and protein prediction using FragGeneScan and Prodigal
• Functional annotation with various databases
• Statistical tests to identify differential abundance of taxonomies and biological functions between samples, with rich visualisations for interpretation
• Quality control and assessment of microbiome data

Genome Analysis Module

• Quality control and trimming using FastQC and Trimmomatic
• De-novo whole genome assembly using ABySS, SPAdes, and Flye
• Read alignment using BWA and Bowtie2
• Repeat identification and masking prior to gene prediction
• Gene finding and coding potential assessment
• Multi-locus Sequence Typing (MLST) support
• Genome annotation visualisation through tracks combining genome sequences, alignments, intron-exon structure, and variant data
• Genome curation tools for newly sequenced genomes

Base Platform Features

• Workflow design, execution, and saving for reproducible analyses
• Integrated genome browser for visualising genomic data
• FastQC quality control tools
• Generic charts including bar, pie, and Venn diagrams
• File manager with support for all major bioinformatics file formats
• Barcode demultiplexing with Cutadapt
• Access to cloud computing resources for large-scale data processing
• Filter and sort large data tables

OmicsBox is available as a subscription and runs natively on Windows, Linux, and Mac without requiring individual tool installation. The platform's cloud computing integration enables processing of large and complex datasets efficiently, making it suitable for both small research groups and large institutions. BioBam offers personalised demo sessions and dedicated support to help researchers get started and optimise their analysis workflows.