PipeBio

PipeBio is a cloud-based bioinformatics platform purpose-built for scientists and bioinformaticians working in antibody, TCR, and peptide discovery and engineering. The platform supports analysis of BCR, TCR, VHH, scFv, and peptide sequences, enabling researchers to process NGS, single-cell, and Sanger sequencing data with speed and reliability. PipeBio serves a broad range of customers, from academic institutions to top-10 pharmaceutical companies. Notably, PipeBio has been acquired by Benchling, reflecting a shared vision for advancing biologics discovery.

The platform is designed to take researchers from raw repertoire data all the way to a refined hit list, automating workflows for identifying candidate sequences from large-scale NGS antibody repertoires, hybridoma sequencing, clonal expansion in biopanning experiments, liability identification, and antibody developability assessment.

Core Platform Capabilities

• Sequence Annotation and Liability Detection: Identify framework regions (FRs), complementarity-determining regions (CDRs), and mutations through germline alignments for antibody formats including IgG, scFv, VHH, and TCRs, as well as custom scaffolds across any species. Detect sequence-based liabilities and align sequences to identify conserved residues and variability.
• Clustering and Sample Comparison: Define clonotypes, identify clonal families, and compare samples across experiments. Analyze enrichment and explore clusters visually using cluster network plots.
• Data Visualization: Use interactive charts to visualize sequence clusters, amino acid frequencies, codons and genes, sequence quality, and phylogeny of antibody clones.
• Functional Assay Data Integration and Hit Picking: Associate functional assay data or metadata with sequences and analyze protein properties, ELISA results, structural liabilities, and transcriptomics data to support hit picking workflows.
• Antibody Engineering: Edit sequences at the nucleotide or protein level, calculate protein properties, optimize degenerate codons for synthesis, and analyze hydrophobicity of sequences using dedicated antibody engineering tools.
• REST API Integration: Integrate with ELN and LIMS systems, internal tools, and third-party platforms. Upload and download data programmatically and build fully automated end-to-end pipelines through the PipeBio REST API.

Sequence Database and Storage

• Store antibody sequences in a centralized database with associated metadata such as target specificity and binding affinity.
• Compare sequences from new experiments against sequences stored in your own database or publicly available databases.
• Supports structured data management to facilitate longitudinal tracking and cross-experiment analysis.

Workflow Automation and Integration

• Configure end-to-end standardized sequence analysis pipelines that can be executed with just a few clicks.
• Integrate seamlessly with existing ELN, LIMS, and internal laboratory tools.
• Build and deploy fully automated bioinformatics pipelines using the platform's REST API.

PipeBio provides a comprehensive, scientist-friendly bioinformatics environment that bridges the gap between raw sequencing data and actionable biological insights, supporting the full antibody and biologics discovery workflow from repertoire analysis through to candidate engineering and selection.