ERGO 2.0

ERGO 2.0 is a systems biology informatics toolkit developed by Igenbio that centres on comparative genomics to capture, query, and visualise sequenced genomes. Using Igenbio's proprietary algorithms and an integrated genomic database, ERGO 2.0 assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterised genes, cryptic pathways, and gene products. The platform is used by scientists in the biotechnology, agriculture, and pharmaceutical industries to understand and design biological systems for new product development.

ERGO 2.0 combines hand-curated content with genomics and bioinformatics tools, and is backed by a database of over 3,000 annotated genomes alongside the largest collection of microbial metabolic and non-metabolic pathways. It supports both prokaryotic and eukaryotic genome analysis and is available via secure cloud access or on-premises installation.

Core Analysis Capabilities

• Whole Genome Annotation: Uses proprietary algorithms, sequence similarity, gene context clustering, and regulatory and expression data to deduce the core functionality of prokaryotic and eukaryotic genomes, supporting both automated and manual annotation.
• Metagenome and Microbiome Analysis: Accepts BIOM file input via drag-and-drop. Computes Principal Coordinates Analysis (PCoA), Richness Estimates, Taxonomic Bar Charts, Analysis of Similarities (ANOSIM), PERMANOVA, Non-metric Multidimensional Scaling (NMDS), Linear Discriminant Analysis (LEfSe), and functional metagenome prediction using PICRUSt2 for 16S amplicon sequencing data.
• Differential Gene Expression Analysis: Integrates expression data from RNA-Seq, cDNA, EST, Microarray, and other sources. Automatically performs statistical analysis and presents differentially expressed genes in their metabolic context, with visualisation on KEGG pathway maps. No prior knowledge of statistical tools is required.
• Variant Detection and Analysis: Identifies and annotates Single Nucleotide Polymorphisms (SNPs), Insertions, and Deletions (InDels), and detects ablated transcripts, frameshifts, and start/stop codon loss.
• Metabolic Analysis: Deduces the core metabolic functionality of a whole organism from genome sequence data to support strain improvement, optimisation, and product development.
• Comparative Genomics: Provides a Genome Align tool for visual exploration of strain differences, and comparative protein clustering tools to identify common and unique clusters or ORFs, including features useful for primer generation across groups of organisms.
• Metabolomics Data Integration: Supports integration of metabolomics data as a recently added feature.

Genomics Tools

• Multiple sequence alignment
• Pairwise sequence alignment
• Creating and viewing taxonomic trees
• Genome alignment
• Automated and manual genome annotation
• Genome Browser for visualising genomes by functional systems or subsystems, including metabolic and non-metabolic pathway distribution, genome plasticity, gene displacement, and orthologous displacements

ERGO Workflows

• Drag-and-drop sequence file input for streamlined analysis
• Supports RNA-Seq analysis and variant analysis workflows
• Designed for straightforward use without requiring command-line expertise

Integrated Databases

• ERGO proprietary database of 3,000+ annotated genomes
• KEGG Pathway Database (licensed from Pathway Solutions, Inc.)
• MetaCyc, EcoCyc, and BioCyc databases (licensed from SRI International)
• Gene Ontology
• RefSeq
• SwissProt
• UniProt

Supported File Formats

• Genome Feature Format (GFF V2/V3)
• FASTA
• GenBank
• CSV/Text
• Variant Files (VCF/BCF)

Visualisation Features

• Genome Browser with functional and subsystem views
• Taxonomic bar charts and ordination plots for microbiome analysis
• Violin plots for expression analysis, using kernel density estimation to visualise log fold change distributions
• KEGG pathway map overlays for expression data

ERGO 2.0 is accessible via a secure cloud platform with data encrypted at rest and in transit, and is also available as a private cloud or on-premises installation. A REST API allows integration with existing tools and infrastructure. A 14-day free trial is available, and licensing and pricing information can be requested directly from Igenbio. The platform has been cited in hundreds of peer-reviewed publications across fields including metagenomics, pathogenomics, synthetic biology, food and agriculture, and industrial biotechnology.